Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008824.1 Hibiscus syriacus cultivar Beakdansim tig00111996_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: 4603428
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 19
Found at i:1008607 original size:19 final size:19
Alignment explanation
Indices: 1008583--1008657 Score: 79
Period size: 19 Copynumber: 4.2 Consensus size: 19
1008573 GCAACGAGAG
*
1008583 AATCGCAATGCGAAATCAA
1 AATCGCAATGCGAAATGAA
*
1008602 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
1008616 AATCGCAATGCGAAATAAA
1 AATCGCAATGCGAAATGAA
*
1008635 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1008654 AATC
1 AATC
1008658 TTAACAACAA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
14 9 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 30 0.67
ACGTcount: A:0.48, C:0.20, G:0.19, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1008612 original size:33 final size:33
Alignment explanation
Indices: 1008570--1008644 Score: 141
Period size: 33 Copynumber: 2.3 Consensus size: 33
1008560 GAAACTGACT
*
1008570 ATCGCAACGAGAGAATCGCAATGCGAAATCAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATAAAA
1008603 ATCGCAACGAGAGAATCGCAATGCGAAATAAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATAAAA
1008636 ATCGCAACG
1 ATCGCAACG
1008645 CGAAATGAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.12
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCGCAATGCGAAATAAAA
Found at i:1008681 original size:52 final size:50
Alignment explanation
Indices: 1008583--1008710 Score: 123
Period size: 52 Copynumber: 2.5 Consensus size: 50
1008573 GCAACGAGAG
* * * * * *
1008583 AATCGCAATGCGAAATCAAAATCGCAACGAGAGAATCGCAATGCGAAA-TAAA
1 AATCGCAACGCGAAAT-AAAATCGCAACAACAAAATCACAACGCGAAACT--A
**
1008635 AATCGCAACGCGAAATGAAAATCTTAACAACAAAATCACAACGCGAAACTA
1 AATCGCAACGCGAAAT-AAAATCGCAACAACAAAATCACAACGCGAAACTA
*
1008686 AATGGCAACGCGAAACTAAAATCGC
1 AATCGCAACGCGAAA-TAAAATCGC
1008711 GCTGCGATTT
Statistics
Matches: 62, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
51 21 0.34
52 40 0.65
53 1 0.02
ACGTcount: A:0.48, C:0.22, G:0.16, T:0.13
Consensus pattern (50 bp):
AATCGCAACGCGAAATAAAATCGCAACAACAAAATCACAACGCGAAACTA
Found at i:1009743 original size:24 final size:24
Alignment explanation
Indices: 1009685--1009731 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1009675 AGTCAGTATT
* *
1009685 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATATTGGTCAATACC
1009709 CGAACTTTGATATTGGTCAATAC
1 CGAACTTTGATATTGGTCAATAC
1009732 TCGGATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATATTGGTCAATACC
Found at i:1009935 original size:12 final size:12
Alignment explanation
Indices: 1009918--1009942 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1009908 ATATAATCCT
1009918 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1009930 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1009942 G
1 G
1009943 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1012240 original size:19 final size:19
Alignment explanation
Indices: 1012216--1012312 Score: 79
Period size: 19 Copynumber: 5.6 Consensus size: 19
1012206 TCATTTGACC
1012216 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1012235 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1012249 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* **
1012268 ATCCCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
1012282 ATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1012301 ATCGCAATGCGA
1 ATCGCAATGCGA
1012313 TTTTAGTTTC
Statistics
Matches: 59, Mismatches: 9, Indels: 20
0.67 0.10 0.23
Matches are distributed among these distances:
14 18 0.31
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 29 0.49
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1012258 original size:33 final size:33
Alignment explanation
Indices: 1012216--1012307 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
1012206 TCATTTGACC
1012216 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1012249 ATCGCAATGCGAAATGAAAATCCCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1012282 ATCGCAAAGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1012308 TGCGATTTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1012356 original size:33 final size:33
Alignment explanation
Indices: 1012308--1012431 Score: 187
Period size: 33 Copynumber: 3.8 Consensus size: 33
1012298 AAAATCGCAA
* * *
1012308 TGCGATTTT-AGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTCA-TTTCGCATTGCGATTCTCTCGT
*
1012341 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
1012374 TGCGATTTTCATTTCGCATTGCGATTCTCTCAT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1012407 TGCGATTTTCATTTCGCATTGCGAT
1 TGCGATTTTCATTTCGCATTGCGAT
1012432 AGTCATTTTT
Statistics
Matches: 86, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
33 85 0.99
34 1 0.01
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:1012362 original size:19 final size:19
Alignment explanation
Indices: 1012340--1012431 Score: 87
Period size: 19 Copynumber: 5.4 Consensus size: 19
1012330 GATTTTGTCG
*
1012340 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
*
1012359 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1012373 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1012392 TTGCGA--TTC---TCTCA
1 TTGCGATTTTCATTTCGCA
1012406 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1012425 TTGCGAT
1 TTGCGAT
1012432 AGTCATTTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 16 0.27
16 10 0.17
17 10 0.17
19 23 0.39
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1012376 original size:14 final size:14
Alignment explanation
Indices: 1012357--1012413 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1012347 TTTCATTTCG
1012357 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1012371 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
1012388 CGCATTGCGATTCTCT
1 CG--TTGCGATTCTCT
*
1012404 CATTGCGATT
1 CGTTGCGATT
1012414 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 7 0.20
19 6 0.17
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1012557 original size:14 final size:14
Alignment explanation
Indices: 1012538--1012574 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1012528 CATCAATTAA
1012538 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1012552 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1012566 ACAAATCAA
1 ACAAATCAA
1012575 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1014502 original size:94 final size:93
Alignment explanation
Indices: 1014325--1014538 Score: 365
Period size: 94 Copynumber: 2.3 Consensus size: 93
1014315 GAATAGTTTC
*
1014325 AATTGGCAGCAAACGAACAAATTTACTTTCAACCAAAAGCAAAACAAAGACAAATACTAACTTCA
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGCAAAACAAAGACAAATACTAACTTCA
* *
1014390 CAGTGTTAAAGAATACACAGTTTAGCAG
66 CAGTGATAAAGAACACACAGTTTAGCAG
*
1014418 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAATCAAAGACAAATACTAACTTC
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAG-CAAAACAAAGACAAATACTAACTTC
1014483 ACAGTGATAAAGAACACACAGTTTAGCAG
65 ACAGTGATAAAGAACACACAGTTTAGCAG
* *
1014512 AATTGGCAGCAACTGAATAAATTTACT
1 AATTGGCAGCAACCGAACAAATTTACT
1014539 AAGCAATCTA
Statistics
Matches: 114, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
93 38 0.33
94 76 0.67
ACGTcount: A:0.46, C:0.20, G:0.13, T:0.21
Consensus pattern (93 bp):
AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGCAAAACAAAGACAAATACTAACTTCA
CAGTGATAAAGAACACACAGTTTAGCAG
Found at i:1016271 original size:19 final size:19
Alignment explanation
Indices: 1016225--1016350 Score: 137
Period size: 19 Copynumber: 7.1 Consensus size: 19
1016215 TCTTTTGGTT
*
1016225 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
1016244 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
1016264 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
1016281 G--A-GATAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1016297 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
1016314 G--A-GATAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1016330 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1016349 GA
1 GA
1016351 TTTTGGTTTC
Statistics
Matches: 90, Mismatches: 6, Indels: 22
0.76 0.05 0.19
Matches are distributed among these distances:
14 20 0.22
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 40 0.44
20 18 0.20
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1016291 original size:14 final size:14
Alignment explanation
Indices: 1016272--1016328 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1016262 GCGAAATGAA
1016272 AATCGCAACGAGAT
1 AATCGCAACGAGAT
*
1016286 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAT
1016305 AATCGCAACGAGAT
1 AATCGCAACGAGAT
1016319 AATCGCAACG
1 AATCGCAACG
1016329 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAGAT
Found at i:1016295 original size:33 final size:33
Alignment explanation
Indices: 1016225--1016345 Score: 188
Period size: 33 Copynumber: 3.5 Consensus size: 33
1016215 TCTTTTGGTT
1016225 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAAC--GAG-AT---AATCGCAACGC
1016264 GAAATGAAAATCGCAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGATAATCGCAACGC
1016297 GAAATGAAAATCGCAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGATAATCGCAACGC
1016330 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1016346 TGCGATTTTG
Statistics
Matches: 82, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
33 60 0.73
36 2 0.02
37 3 0.04
39 17 0.21
ACGTcount: A:0.48, C:0.19, G:0.21, T:0.12
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGATAATCGCAACGC
Found at i:1016381 original size:14 final size:14
Alignment explanation
Indices: 1016362--1016418 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1016352 TTTGGTTTCG
1016362 CGTTGCGATTATCT
1 CGTTGCGATTATCT
*
1016376 CGTTGCGATTTTCATTTT
1 CGTTGCGA--TT-A-TCT
*
1016394 GCATTGCGATTATCT
1 -CGTTGCGATTATCT
1016409 CGTTGCGATT
1 CGTTGCGATT
1016419 TTCATTCTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 17 0.50
15 2 0.06
16 3 0.09
17 3 0.09
18 2 0.06
19 7 0.21
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTATCT
Found at i:1016401 original size:33 final size:33
Alignment explanation
Indices: 1016346--1016424 Score: 122
Period size: 33 Copynumber: 2.4 Consensus size: 33
1016336 AAAATCGCAA
** *
1016346 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTATCTCGT
*
1016379 TGCGATTTTCATTTTGCATTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTATCTCGT
1016412 TGCGATTTTCATT
1 TGCGATTTTCATT
1016425 CTCTCGTTGC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTATCTCGT
Found at i:1016431 original size:20 final size:20
Alignment explanation
Indices: 1016406--1016467 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
1016396 ATTGCGATTA
1016406 TCTCGTTGCGATTTTCATTC
1 TCTCGTTGCGATTTTCATTC
**
1016426 TCTCGTTGCGATAGTCATT-
1 TCTCGTTGCGATTTTCATTC
*
1016445 TCCGCGTTGCGATTTTCATTC
1 T-CTCGTTGCGATTTTCATTC
1016466 TC
1 TC
1016468 GAAACTATTC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.03
20 33 0.94
21 1 0.03
ACGTcount: A:0.11, C:0.26, G:0.18, T:0.45
Consensus pattern (20 bp):
TCTCGTTGCGATTTTCATTC
Found at i:1018260 original size:2 final size:2
Alignment explanation
Indices: 1018253--1018299 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1018243 TATATTTAAA
1018253 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
1018295 A- AT AT
1 AT AT AT
1018300 TAATATTATT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1019499 original size:174 final size:176
Alignment explanation
Indices: 1019180--1019880 Score: 1125
Period size: 174 Copynumber: 4.0 Consensus size: 176
1019170 CATCGTAAAG
* * *
1019180 TCTCATAGAATAGATAACCACATAGCTCAACCTTTTTTGTTGTTTCTTC-TTATTTCTTTCTTCT
1 TCTCATAGAACAGATAACCACATAGCTCAACCTTTTTTGTTGCTTCTTCTTTCTTTCTTTCTTCT
* * * *
1019244 TTTTCTCCTCATCCTCATCCTTCTTCTTCTTACAAAGTCTACTATTCTTTCTCCTCCATGTTTAA
66 TTTTCTCCTCATCCTCCT-CTTCTTATTCTTGCAAAGTCTGCTATTCTTTCTCCTCCATGTTTAA
1019309 TTATTAATAATATTTGGATACCATGATACACACTTCTTTCCTGATCT
130 TTATTAATAATATTTGGATACCATGATACACACTTCTTTCCTGATCT
1019356 TCTCATAGAACAGATAACCACATAGCTCAACCTTTTTTGTTGCTTCTTCTTTCTTTCTTTCTTCT
1 TCTCATAGAACAGATAACCACATAGCTCAACCTTTTTTGTTGCTTCTTCTTTCTTTCTTTCTTCT
1019421 TTTTCTCCTCATCCTCCTC-T-TTATTCTTGCAAAGTCTGCTATTCTTTCTCCTCCATGTTTAAT
66 TTTTCTCCTCATCCTCCTCTTCTTATTCTTGCAAAGTCTGCTATTCTTTCTCCTCCATGTTTAAT
1019484 TATTAATAATATTTGGATACCATGATACACACTTCTTT-CTCGATCT
131 TATTAATAATATTTGGATACCATGATACACACTTCTTTCCT-GATCT
* *
1019530 TCTCATAGAACAGATAACCACATAGCTCAACCTTTTTTGTTGCTTCTTTTTTTTTTC-TT-TT-T
1 TCTCATAGAACAGATAACCACATAGCTCAACCTTTTTTGTTGCTTCTTCTTTCTTTCTTTCTTCT
* *
1019592 TTTTCTCCT-ATTCTTCCTCTTTCTTATTCTTGCAAAGTTTGCTATTCTTTCTCCTCCATGTTTA
66 TTTTCTCCTCA-TCCTCCTC-TTCTTATTCTTGCAAAGTCTGCTATTCTTTCTCCTCCATGTTTA
1019656 ATTATTAATAATATTTGGATACCATGATACACACTTCTTTCCTGATCT
129 ATTATTAATAATATTTGGATACCATGATACACACTTCTTTCCTGATCT
* * *
1019704 TCTCATAGAACAGATAACCACGTAGCTCAATCTTTTTTGTTACTTCTTCTTTCTTTCTTTCTTCT
1 TCTCATAGAACAGATAACCACATAGCTCAACCTTTTTTGTTGCTTCTTCTTTCTTTCTTTCTTCT
* *
1019769 TTTTCTCCTCCTCCT-C-CTTCTTATTCTTGCAAAGTCTGATATTCTTTCTCCTCCATGTTTAAT
66 TTTTCTCCTCATCCTCCTCTTCTTATTCTTGCAAAGTCTGCTATTCTTTCTCCTCCATGTTTAAT
* * *
1019832 TATTAATACTCTTTGGATACCATGATACACACTTTTTTCCTGATCT
131 TATTAATAATATTTGGATACCATGATACACACTTCTTTCCTGATCT
1019878 TCT
1 TCT
1019881 AATACTGTAT
Statistics
Matches: 491, Mismatches: 23, Indels: 24
0.91 0.04 0.04
Matches are distributed among these distances:
170 1 0.00
171 17 0.03
172 2 0.00
173 5 0.01
174 365 0.74
175 6 0.01
176 51 0.10
177 44 0.09
ACGTcount: A:0.21, C:0.25, G:0.07, T:0.47
Consensus pattern (176 bp):
TCTCATAGAACAGATAACCACATAGCTCAACCTTTTTTGTTGCTTCTTCTTTCTTTCTTTCTTCT
TTTTCTCCTCATCCTCCTCTTCTTATTCTTGCAAAGTCTGCTATTCTTTCTCCTCCATGTTTAAT
TATTAATAATATTTGGATACCATGATACACACTTCTTTCCTGATCT
Found at i:1022773 original size:15 final size:16
Alignment explanation
Indices: 1022748--1022777 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1022738 TAGTTATCTA
1022748 TTTTACTTTATTTATG
1 TTTTACTTTATTTATG
1022764 TTTT-CTTTATTTAT
1 TTTTACTTTATTTAT
1022778 TGTAGGCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.73
Consensus pattern (16 bp):
TTTTACTTTATTTATG
Found at i:1025791 original size:19 final size:19
Alignment explanation
Indices: 1025767--1025806 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1025757 AGGAGAAAGG
1025767 GTCTGTGTGGATTGTGTAT
1 GTCTGTGTGGATTGTGTAT
1025786 GTCTGTGTGGATTGTGTAT
1 GTCTGTGTGGATTGTGTAT
1025805 GT
1 GT
1025807 GTAGAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.10, C:0.05, G:0.38, T:0.47
Consensus pattern (19 bp):
GTCTGTGTGGATTGTGTAT
Found at i:1035263 original size:20 final size:20
Alignment explanation
Indices: 1035238--1035281 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
1035228 ACACGAATGT
1035238 GTGTCATCTTTTTTAATGAC
1 GTGTCATCTTTTTTAATGAC
1035258 GTGTCATCTTTTTTAATGAC
1 GTGTCATCTTTTTTAATGAC
1035278 GTGT
1 GTGT
1035282 GCTTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.14, G:0.18, T:0.50
Consensus pattern (20 bp):
GTGTCATCTTTTTTAATGAC
Found at i:1035350 original size:41 final size:41
Alignment explanation
Indices: 1035288--1035378 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 41
1035278 GTGTGCTTCA
* ** *
1035288 ATGACACAC-AATGTAAGTCATACATGCGTGTCATATATTT
1 ATGACACACAAATGTAAGTCATAAATGCACGTCATAAATTT
**
1035328 ATGACACACAAATGTGTGTCATAAATGCACGTCATAAATTT
1 ATGACACACAAATGTAAGTCATAAATGCACGTCATAAATTT
*
1035369 ATGACGCACA
1 ATGACACACA
1035379 GTTGCGTGTC
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
40 9 0.21
41 34 0.79
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (41 bp):
ATGACACACAAATGTAAGTCATAAATGCACGTCATAAATTT
Found at i:1061857 original size:726 final size:733
Alignment explanation
Indices: 1060414--1062097 Score: 2462
Period size: 726 Copynumber: 2.3 Consensus size: 733
1060404 CAAGAATGCA
*
1060414 AAAGTTGAGTTTTATTATTTTGAGCAACCATACATTGAAACAAATCAATATAATCAACAAAAGAT
1 AAAGTTGAGTTTTATTATTTTGAGCAACCATACAATG----AAA-C---A-AATCAACAAAAGAT
* *
1060479 AATGAAACAGAATAAAGAGTTTTAGCATTGAGTTTATTGAAAGAAGACCCAAACAAGTACAATCC
57 AATGAAACAGAACAAACAGTTTTAGCATTGAGTTTATTGAAAGAAGACCCAAACAAGTACAATCC
* * *
1060544 TTTGAACTCCTTACCAATTCCCTTCATCTTGCCAGTGGAAAGATACTGCAAGATGCAGAAATCAA
122 TTTGAACTCCTTACCAATTCCCTTAATCTTGCCAGTGGAAAGATCCTGCATGATGCAGAAATCAA
* * * *
1060609 GGT-AAAAATAATTGCACAATTAGATCACGGGATAATTTGGAAATGAAAAGAAGATTATGTGTAA
187 GGTAAAAAATAATTCCAAAATTAGATCACAGGATAATTTGGAAATGAAAAGAAGATTATATGTAA
* * * * *
1060673 ATTGACGAACAAACAAAACATTTTTCAAAGAGATATCAAGTTATAGAAGATCTTGAATGAGTAAT
252 ATTGACGAACAAACAAAACATTGTTAAAAAAGATATCAAGTTATAAAAGATCTTGAATAAGTAAT
* * *
1060738 AAGAGTATTTTTACCATCCAGTTGGCGAACAAAACGAGGAACAAGATTACAATCAACATGATTAA
317 AAGAGAATTTTTACCA-CCAGTAGGCGAACAAAACGAGAAACAAGATTACAATCAACATGATTAA
* *
1060803 TTAAGTTTTTAGAACTAGATAAAAATGGTCAATTACCCCAGTATCCAAAATCCAGTTATTGGAAG
381 TCAAGTTTCTAGAACTAGATAAAAATGGTCAATTACCCCAGTATCCAAAATCCAGTTATTGGAAG
* * *
1060868 CATCAATAACAAATGAAGAATATGCAATACCTGGAAGATGTGCAACAAAATCAACATAAGGCAGT
446 CATCAATAACAAATGAAGAAGATGCAATACCTGCAAGATGTGCAACAAAATCAACATAAGCCAGT
* * *
1060933 TTGGCCTATAACCCCAAGACATGTTTATACTGAGCTATAATTAATGTAGGAGCACTGAAACCCCC
511 TTGGCCTACAACCCCAAGACATGTTTATACTGAGCTACAATTAATGTAAGAGCACTGAAACCCCC
1060998 AAAATCAACTCTTGACACATGGGAAACATCACAATCACCATCACCACTAGCTTCTGCGAGATTGA
576 AAAATCAACTCTTGACACATGGGAAACAT-ACAATCA-CATCACCACTAGCTTCTGCGAGATTGA
* *
1061063 TCTGCGAAGGCTTCTTATTAAACTTTAAATCTGAAAGAAATCCAATAATGTGATAACAAAGGGTA
639 CCTGCGAAGGCTTCTTATTAAACGTTAAATCTGAAAGAAATCCAATAATGTGATAACAAAGGGTA
1061128 AATGACAC-A-T-AT-TA-G-AA-A-AATG
704 AATGACACTATTAATGTATGCAACAGAATG
*
1061150 -AATTTGAGTTTTATTATTTTGAGCAACCATACAATGAAACAAATCAACAAAAGATAATGAAACA
1 AAAGTTGAGTTTTATTATTTTGAGCAACCATACAATGAAACAAATCAACAAAAGATAATGAAACA
*
1061214 GAACAAACAGTTTTAGCATTGAGTTTATTGAAAGAAGACCCAAACAAGTGCAATCCTTTGAACTC
66 GAACAAACAGTTTTAGCATTGAGTTTATTGAAAGAAGACCCAAACAAGTACAATCCTTTGAACTC
* *
1061279 CTTTCCAATTCCCTTAATCTTGCTAGTGGAAAGATCCTGCATGATGCAGAAATCAAGGTAAAAAA
131 CTTACCAATTCCCTTAATCTTGCCAGTGGAAAGATCCTGCATGATGCAGAAATCAAGGTAAAAAA
* *
1061344 TAATTCCAAAATTTAGATCACAGGTTAATTTGGAAATGAAAAGAAGATTATATGTAAATTGAGGA
196 TAATTCCAAAA-TTAGATCACAGGATAATTTGGAAATGAAAAGAAGATTATATGTAAATTGACGA
*
1061409 ACAAACAAAACATTGTTAAAAAAGATATCAAGTTGTAAAAGATCTTGAATAAGTAATAAGAGAAT
260 ACAAACAAAACATTGTTAAAAAAGATATCAAGTTATAAAAGATCTTGAATAAGTAATAAGAGAAT
* * * *
1061474 TTTTACCA-CATGGTAGGCTAGCCAAACGAGAAACAAGATTACAATCAATATGATTAATCAAGTT
325 TTTTACCACCA--GTAGGCGAACAAAACGAGAAACAAGATTACAATCAACATGATTAATCAAGTT
* *
1061538 TCTAGAACTAGATAAAAAAAATGGTCAATTACCCCTAGTATCCAAATTCCAGTTCTTGGAAGCAT
388 TCTAGAACTAGAT---AAAAATGGTCAATTACCCC-AGTATCCAAAATCCAGTTATTGGAAGCAT
* *
1061603 CAATAACAAATGAAGAAGATGCAATACCTGCAAGATTTTCAACAAAATCAACATAAGCCAGTTTG
449 CAATAACAAATGAAGAAGATGCAATACCTGCAAGATGTGCAACAAAATCAACATAAGCCAGTTTG
* * *
1061668 GCCTACAGCCCCAAGACATGTTTATACTGAGCTACAATTAATGTAAGTGCACTGAAACCCCCTAA
514 GCCTACAACCCCAAGACATGTTTATACTGAGCTACAATTAATGTAAGAGCACTGAAACCCCCAAA
*
1061733 ATCAACTCTTGACACATGGGAAACAT-C-A-CA-ATCACCACTAGCTTCTGTGAGATTGACCTGC
579 ATCAACTCTTGACACATGGGAAACATACAATCACATCACCACTAGCTTCTGCGAGATTGACCTGC
* *
1061794 GAAGGCTTCTTATTAAACGTTAAATCTGACAGAAATCCAATAATGTGATAATAAAGGGTAAATGA
644 GAAGGCTTCTTATTAAACGTTAAATCTGAAAGAAATCCAATAATGTGATAACAAAGGGTAAATGA
1061859 CACTTATTAGAAACATGAGTATGCCTAACCCAGAATG
709 CAC-TATT----A-AT--GTATG-C-AA--CAGAATG
1061896 CAAAAGTTGAGTTTTATTATTTTGAGCAACCATACAATGAAACAAATCAACAAAAGATAATGAAA
1 --AAAGTTGAGTTTTATTATTTTGAGCAACCATACAATGAAACAAATCAACAAAAGATAATGAAA
* * * *
1061961 TAGAACAAACAGTTTTAGCATTGAGTTTATTGAAAGGAGACCCAAACATGTACAATCATTTGAAC
64 CAGAACAAACAGTTTTAGCATTGAGTTTATTGAAAGAAGACCCAAACAAGTACAATCCTTTGAAC
* * *
1062026 TCCTTACCAATTTCCTTAATCTTGCCAGTTGAAAGATCCTGTATGATGCAGAAATCAAGGTAAAA
129 TCCTTACCAATTCCCTTAATCTTGCCAGTGGAAAGATCCTGCATGATGCAGAAATCAAGGTAAAA
1062091 AATAATT
194 AATAATT
1062098 GTACGATTTA
Statistics
Matches: 857, Mismatches: 60, Indels: 49
0.89 0.06 0.05
Matches are distributed among these distances:
726 235 0.27
727 15 0.02
728 175 0.20
729 2 0.00
730 2 0.00
731 22 0.03
732 172 0.20
735 36 0.04
738 2 0.00
739 1 0.00
742 2 0.00
745 1 0.00
746 4 0.00
749 188 0.22
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.26
Consensus pattern (733 bp):
AAAGTTGAGTTTTATTATTTTGAGCAACCATACAATGAAACAAATCAACAAAAGATAATGAAACA
GAACAAACAGTTTTAGCATTGAGTTTATTGAAAGAAGACCCAAACAAGTACAATCCTTTGAACTC
CTTACCAATTCCCTTAATCTTGCCAGTGGAAAGATCCTGCATGATGCAGAAATCAAGGTAAAAAA
TAATTCCAAAATTAGATCACAGGATAATTTGGAAATGAAAAGAAGATTATATGTAAATTGACGAA
CAAACAAAACATTGTTAAAAAAGATATCAAGTTATAAAAGATCTTGAATAAGTAATAAGAGAATT
TTTACCACCAGTAGGCGAACAAAACGAGAAACAAGATTACAATCAACATGATTAATCAAGTTTCT
AGAACTAGATAAAAATGGTCAATTACCCCAGTATCCAAAATCCAGTTATTGGAAGCATCAATAAC
AAATGAAGAAGATGCAATACCTGCAAGATGTGCAACAAAATCAACATAAGCCAGTTTGGCCTACA
ACCCCAAGACATGTTTATACTGAGCTACAATTAATGTAAGAGCACTGAAACCCCCAAAATCAACT
CTTGACACATGGGAAACATACAATCACATCACCACTAGCTTCTGCGAGATTGACCTGCGAAGGCT
TCTTATTAAACGTTAAATCTGAAAGAAATCCAATAATGTGATAACAAAGGGTAAATGACACTATT
AATGTATGCAACAGAATG
Found at i:1062430 original size:321 final size:310
Alignment explanation
Indices: 1061831--1062434 Score: 868
Period size: 321 Copynumber: 1.9 Consensus size: 310
1061821 GACAGAAATC
* * * * * * *
1061831 CAATAATGTGATAATAAAGGGTAAATGACACTTATTAGAAACATGAGTATGCCTAACCCAGAATG
1 CAATAAGGTGATAACAAAAGGTAAATGACAATTATTAGAAAAATGAATATGCCTAACCAAGAATG
1061896 CAAAAGTTGAGTTTTATTATTTTGAGCAACCATACAATGAAACAAATCAACAAAAGATAATGAAA
66 CAAAAGTTGAGTTTTATTATTTTGAGCAACCATACAATGAAACAAATCAACAAAAGATAATGAAA
* ** * *
1061961 TAGAACAAACAGTTTTAGCATTGAGTTTATTGAAAGGAGACCCAAACATGTACAATCATTTGAAC
131 CAGAACAAACAAATTTAGCATTGAGTTTATTGAAAGAAGACCCAAACAAGTACAATCATTTGAAC
* * ** *
1062026 TCCTTACCAATTTCCTTAATCTTGCCAGTTGAAAGATCCTGTATGATGCAGAAATCAAGGTAAAA
196 TCCTTACCAATTCCCTTAATCTTGCCAGTGGAAAGATCCTACATGATACAGAAATCAAGGTAAAA
* *
1062091 AATAATTGTACGATTTAAGATCAATTATTTTTTTACAATTAACTTGATTA
261 AATAATTGCACAATTTAAGATCAATTATTTTTTTACAATTAACTTGATTA
1062141 CAATAAGGTGATAACAAAAGGTAAATGA-AATATATTAGAAAAATGAATATTGCCTAACCAAGAA
1 CAATAAGGTGATAACAAAAGGTAAATGACAAT-TATTAGAAAAATGAATA-TGCCTAACCAAGAA
*
1062205 TGCAAAAGTTGAGTTTTATTATTTTGAGCAACCATACAATAAAATAAATCAACAGAGTCAACAAA
64 TGCAAAAGTTGAGTTTTATTATTTTGAGCAACCATACAAT----GAAA-C-A-A-A-TCAACAAA
1062270 AGATAATGAAACAGAACAAACAAATTTAGCATTGAGTTTATTGAAAGAAGACCCAAACAAGTAAC
120 AGATAATGAAACAGAACAAACAAATTTAGCATTGAGTTTATTGAAAGAAGACCCAAACAAGT-AC
* * * *
1062335 AATCCTTTGAACTCCTTACCAATTCCCTTCATCTTGCCAGTGGGAAGATCCTACATGATACATAA
184 AATCATTTGAACTCCTTACCAATTCCCTTAATCTTGCCAGTGGAAAGATCCTACATGATACAGAA
*
1062400 ATCAAGGTAAAGAATAATTGCACAATTTAAGATCA
249 ATCAAGGTAAAAAATAATTGCACAATTTAAGATCA
1062435 TGGGTTACAT
Statistics
Matches: 257, Mismatches: 25, Indels: 13
0.87 0.08 0.04
Matches are distributed among these distances:
309 2 0.01
310 40 0.16
311 53 0.21
315 3 0.01
316 1 0.00
317 1 0.00
318 1 0.00
319 1 0.00
320 65 0.25
321 90 0.35
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (310 bp):
CAATAAGGTGATAACAAAAGGTAAATGACAATTATTAGAAAAATGAATATGCCTAACCAAGAATG
CAAAAGTTGAGTTTTATTATTTTGAGCAACCATACAATGAAACAAATCAACAAAAGATAATGAAA
CAGAACAAACAAATTTAGCATTGAGTTTATTGAAAGAAGACCCAAACAAGTACAATCATTTGAAC
TCCTTACCAATTCCCTTAATCTTGCCAGTGGAAAGATCCTACATGATACAGAAATCAAGGTAAAA
AATAATTGCACAATTTAAGATCAATTATTTTTTTACAATTAACTTGATTA
Found at i:1062450 original size:47 final size:47
Alignment explanation
Indices: 1062393--1062488 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
1062383 TCCTACATGA
1062393 TACATAAATCAAGGTAAAGAATAATTGCACAATTTAAGATCATGGGT
1 TACATAAATCAAGGTAAAGAATAATTGCACAATTTAAGATCATGGGT
1062440 TACATAAATCAAGGTAAAGAATAATTGCACAATTTAAGATCATGGGT
1 TACATAAATCAAGGTAAAGAATAATTGCACAATTTAAGATCATGGGT
1062487 TA
1 TA
1062489 ATTTGGAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.28
Consensus pattern (47 bp):
TACATAAATCAAGGTAAAGAATAATTGCACAATTTAAGATCATGGGT
Found at i:1068378 original size:27 final size:28
Alignment explanation
Indices: 1068327--1068379 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
1068317 TAACTTCATT
* *
1068327 TTTTTAATTTTTTAATTATAATTTTAGA
1 TTTTAAATTTTTAAATTATAATTTTAGA
*
1068355 TTTTAAATTTTTAAATT-TATTTTTA
1 TTTTAAATTTTTAAATTATAATTTTA
1068380 AAAATAGCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 7 0.32
28 15 0.68
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (28 bp):
TTTTAAATTTTTAAATTATAATTTTAGA
Found at i:1068438 original size:13 final size:14
Alignment explanation
Indices: 1068416--1068452 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1068406 TGTAAATTCA
1068416 TTTAATTTTTTA-AT
1 TTTAA-TTTTTAGAT
1068430 TTTAA-TTTTAGAT
1 TTTAATTTTTAGAT
1068443 TTTAATTTTT
1 TTTAATTTTT
1068453 TTAAATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 5 0.24
13 7 0.33
14 9 0.43
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (14 bp):
TTTAATTTTTAGAT
Found at i:1069114 original size:21 final size:20
Alignment explanation
Indices: 1069086--1069127 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1069076 TGTACAAATG
*
1069086 GAAACCCTCCCACAATCCTC
1 GAAACCCTCCCACAACCCTC
*
1069106 GAAAGCCCTCCCTCAACCCTC
1 GAAA-CCCTCCCACAACCCTC
1069127 G
1 G
1069128 GAAGACAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.26, C:0.50, G:0.10, T:0.14
Consensus pattern (20 bp):
GAAACCCTCCCACAACCCTC
Found at i:1072708 original size:15 final size:15
Alignment explanation
Indices: 1072688--1072720 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1072678 TAAAGACGAC
1072688 TTTCTTGCACAGTGA
1 TTTCTTGCACAGTGA
1072703 TTTCTTGCACAGTGA
1 TTTCTTGCACAGTGA
1072718 TTT
1 TTT
1072721 AGAATAGGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (15 bp):
TTTCTTGCACAGTGA
Found at i:1075254 original size:25 final size:25
Alignment explanation
Indices: 1075220--1075269 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1075210 TCTACCTATA
*
1075220 ATATATTATTCTTGTGGTAGATATG
1 ATATATTATTATTGTGGTAGATATG
*
1075245 ATATGTTATTATTGTGGTAGATATG
1 ATATATTATTATTGTGGTAGATATG
1075270 GTATTGTCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.28, C:0.02, G:0.22, T:0.48
Consensus pattern (25 bp):
ATATATTATTATTGTGGTAGATATG
Found at i:1082088 original size:14 final size:15
Alignment explanation
Indices: 1082055--1082089 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1082045 TTGCTCTCAA
1082055 TTTTCTCACTAAAGC
1 TTTTCTCACTAAAGC
*
1082070 TTTTCTCTCTAAA-C
1 TTTTCTCACTAAAGC
1082084 TTTTCT
1 TTTTCT
1082090 TTGTGTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.20, C:0.26, G:0.03, T:0.51
Consensus pattern (15 bp):
TTTTCTCACTAAAGC
Found at i:1086494 original size:14 final size:15
Alignment explanation
Indices: 1086464--1086498 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
1086454 TTGCTCTCAA
1086464 TTTTCTCACTAAAGC
1 TTTTCTCACTAAAGC
*
1086479 TTTTCTCTCT-AAGC
1 TTTTCTCACTAAAGC
1086493 TTTTCT
1 TTTTCT
1086499 TTGTGTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.17, C:0.26, G:0.06, T:0.51
Consensus pattern (15 bp):
TTTTCTCACTAAAGC
Found at i:1089329 original size:21 final size:22
Alignment explanation
Indices: 1089289--1089329 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1089279 ATTTTTTTAT
*
1089289 ATATTTAATTGTTTAATTTTCC
1 ATATTTAATTATTTAATTTTCC
*
1089311 ATATTT-ATTATTTATTTTT
1 ATATTTAATTATTTAATTTT
1089330 TCTAATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (22 bp):
ATATTTAATTATTTAATTTTCC
Found at i:1094884 original size:38 final size:37
Alignment explanation
Indices: 1094796--1094926 Score: 103
Period size: 36 Copynumber: 3.6 Consensus size: 37
1094786 GGTTCTCTTG
* *
1094796 AAAAATTTT-ATCTCACAT-GAGATAGTTTTTCTT-AAA
1 AAAAATTTTCATCTCAC-TCGAGACAG-TTTCCTTCAAA
* * *
1094832 ATAAA-TTTCGTCTCAATCGAGACAG-TTCCTCTCCAAA
1 AAAAATTTTCATCTCACTCGAGACAGTTTCCT-T-CAAA
* *
1094869 TAAAAATTTT-ATCTCACTTGAGATAGTTTCCTTCAAA
1 -AAAAATTTTCATCTCACTCGAGACAGTTTCCTTCAAA
*
1094906 AACAATTTTCATCTCACTCGA
1 AAAAATTTTCATCTCACTCGA
1094927 AACAAAAATT
Statistics
Matches: 74, Mismatches: 12, Indels: 17
0.72 0.12 0.17
Matches are distributed among these distances:
34 4 0.05
35 5 0.07
36 23 0.31
37 17 0.23
38 17 0.23
39 8 0.11
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (37 bp):
AAAAATTTTCATCTCACTCGAGACAGTTTCCTTCAAA
Found at i:1095017 original size:71 final size:70
Alignment explanation
Indices: 1094922--1095201 Score: 307
Period size: 71 Copynumber: 4.0 Consensus size: 70
1094912 TTTCATCTCA
* *
1094922 CTCGAAACAAAAATTT--TCTCACTTGTGATATTTTCCCTTGAAAATTGTCATCTCACTCGAGAC
1 CTCGAAAC-AAAATTTCATCTCACTTGAGATATTTTCCCTTGAAAATTTTC-TCTCACTCGAGAC
1094985 AGTTTCT
64 AGTTTCT
* * * * *
1094992 CTCGAAACAGAATTTCATCTCACTTGAGATATTTTCCTTTGGAAATTTTTCTCTCACTCAAAACA
1 CTCGAAACAAAATTTCATCTCACTTGAGATATTTTCCCTT-GAAAATTTTCTCTCACTCGAGACA
*
1095057 ATTTCT
65 GTTTCT
** * * * * * *
1095063 CTTAAAACAAAATTCCATATCACTTGAGAGATTTTCTCTTG-AATTTTTTTCTCACTCGAGACAG
1 CTCGAAACAAAATTTCATCTCACTTGAGATATTTTCCCTTGAAAATTTTCTCTCACTCGAGACAG
1095127 TTTCT
66 TTTCT
* * *
1095132 CACGAAACAAAATTTTATCTCACTTGAGATATTTTCCCTTGAAAAATTTTAC-CTCACTCGAAAC
1 CTCGAAACAAAATTTCATCTCACTTGAGATATTTTCCCTTG-AAAATTTT-CTCTCACTCGAGAC
*
1095196 ATTTTC
64 AGTTTC
1095202 CTAACATTAC
Statistics
Matches: 172, Mismatches: 32, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
69 63 0.37
70 9 0.05
71 92 0.53
72 8 0.05
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.38
Consensus pattern (70 bp):
CTCGAAACAAAATTTCATCTCACTTGAGATATTTTCCCTTGAAAATTTTCTCTCACTCGAGACAG
TTTCT
Found at i:1096148 original size:44 final size:43
Alignment explanation
Indices: 1096074--1096245 Score: 186
Period size: 44 Copynumber: 3.9 Consensus size: 43
1096064 TGGCCTAAAA
** *
1096074 AACATTTCAAGTGGCTTAAACACGCAAAGGGGAGTCATCCGAAG
1 AACATTTCACCTGGCTTAAACCCG-AAAGGGGAGTCATCCGAAG
* * *
1096118 AATATTTCACCTGGCTTAAACCCGATAAGGGGATTCATCCAAAG
1 AACATTTCACCTGGCTTAAACCCGA-AAGGGGAGTCATCCGAAG
* * *
1096162 AACATTTCACCTGGCTTAAAAACGCGAAGGGGGAGCCATCCGAAG
1 AACATTTCACCTGGCTT--AAACCCGAAAGGGGAGTCATCCGAAG
*
1096207 AACATTTCACCTAGCTT-AACCC-ATGAAGGGGAGTCATCC
1 AACATTTCACCTGGCTTAAACCCGA--AAGGGGAGTCATCC
1096246 AAAGTTTGAT
Statistics
Matches: 107, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
41 1 0.01
42 4 0.04
43 13 0.12
44 52 0.49
45 30 0.28
46 7 0.07
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (43 bp):
AACATTTCACCTGGCTTAAACCCGAAAGGGGAGTCATCCGAAG
Found at i:1096236 original size:88 final size:88
Alignment explanation
Indices: 1096074--1096249 Score: 248
Period size: 88 Copynumber: 2.0 Consensus size: 88
1096064 TGGCCTAAAA
* * * * *
1096074 AACATTTCAAGTGGCTTAAACACGCAAAGGGGAGTCATCCGAAGAATATTTCACCTGGCTTAAAC
1 AACATTTCAACTGGCTTAAAAACGCAAAGGGGAGCCATCCGAAGAACATTTCACCTAGCTTAAAC
*
1096139 CCGATAAGGGGATTCATCCAAAG
66 CCGATAAGGGGAGTCATCCAAAG
* *
1096162 AACATTTCACCTGGCTTAAAAACGCGAAGGGGGAGCCATCCGAAGAACATTTCACCTAGCTT-AA
1 AACATTTCAACTGGCTTAAAAACGC-AAAGGGGAGCCATCCGAAGAACATTTCACCTAGCTTAAA
1096226 CCC-ATGAAGGGGAGTCATCCAAAG
65 CCCGAT-AAGGGGAGTCATCCAAAG
1096250 TTTGATATGA
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
87 2 0.03
88 44 0.56
89 32 0.41
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (88 bp):
AACATTTCAACTGGCTTAAAAACGCAAAGGGGAGCCATCCGAAGAACATTTCACCTAGCTTAAAC
CCGATAAGGGGAGTCATCCAAAG
Found at i:1102615 original size:54 final size:54
Alignment explanation
Indices: 1102573--1102995 Score: 510
Period size: 54 Copynumber: 7.8 Consensus size: 54
1102563 CCATATGATC
* * * * * * * *
1102573 ATTCATAAACATATTATGAATTTCATGATTTGCACACATAGTGTCAAAACGGTT
1 ATTCATCAACATATGATGAATTTCGTGAATTGCACACTTAGTGCCGAAACGATT
* * *
1102627 ATTCATCAACATATGATGAA-TTCTGTGAATTGCACACATAATGCCGAAACAATT
1 ATTCATCAACATATGATGAATTTC-GTGAATTGCACACTTAGTGCCGAAACGATT
* * *
1102681 ATTCATCAACATATGATGAATTTCGTGAATTGCACACTCAGTGCTGAAAC-AGTA
1 ATTCATCAACATATGATGAATTTCGTGAATTGCACACTTAGTGCCGAAACGA-TT
* * * * *
1102735 ATTCATCAATATATGATGAATTACGTGAAGTACACACTTAGTGCCGAAACAATT
1 ATTCATCAACATATGATGAATTTCGTGAATTGCACACTTAGTGCCGAAACGATT
* * * *
1102789 ATTCATCAACATATGATGACTTTCGTGAAATGCACACTTAGTGCCAAAACGGTT
1 ATTCATCAACATATGATGAATTTCGTGAATTGCACACTTAGTGCCGAAACGATT
* * *
1102843 ATTCATAAACATATGATGAATTTCGTGAATTGCACACTTAGTGCCGAAATGGTT
1 ATTCATCAACATATGATGAATTTCGTGAATTGCACACTTAGTGCCGAAACGATT
* * * *
1102897 ATTCATCAACATATGATGAATTCCGTGAGTTGCACACTTAGTACCAAAACGATT
1 ATTCATCAACATATGATGAATTTCGTGAATTGCACACTTAGTGCCGAAACGATT
* *
1102951 ATTCATCATCATATGATGAA-TTCAGTGAATTGCACAATTAGTGCC
1 ATTCATCAACATATGATGAATTTC-GTGAATTGCACACTTAGTGCC
1102996 TATTTTGTAA
Statistics
Matches: 318, Mismatches: 46, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
53 6 0.02
54 308 0.97
55 4 0.01
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (54 bp):
ATTCATCAACATATGATGAATTTCGTGAATTGCACACTTAGTGCCGAAACGATT
Found at i:1107915 original size:103 final size:105
Alignment explanation
Indices: 1107736--1107944 Score: 395
Period size: 103 Copynumber: 2.0 Consensus size: 105
1107726 TCAGTTTGCA
1107736 CTGATCTCTCCCCGGATCTCTGTGGACAACTCCTAGCATAATGATCCGTTTCTTTATAAATTAAA
1 CTGATCTCTCCCCGGATCTCTGTGGACAACTCCTAGCATAATGATCCGTTTCTTTATAAATTAAA
1107801 CAAGCCCCATAGAACACTCTAC-A-TCCCCGATGAAATTT
66 CAAGCCCCATAGAACACTCTACAACTCCCCGATGAAATTT
1107839 CTGATCTCTCCCCGGATCTCTGTGGACAACTCCTAGCATAATGATCCGTTTCTTTATAAATTAAA
1 CTGATCTCTCCCCGGATCTCTGTGGACAACTCCTAGCATAATGATCCGTTTCTTTATAAATTAAA
1107904 CAAGCCCCATAGAACACTCTACATACTCCCCGATGAAATTT
66 CAAGCCCCATAGAACACTCTACA-ACTCCCCGATGAAATTT
1107945 TCCACATGAT
Statistics
Matches: 103, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
103 87 0.84
105 1 0.01
106 15 0.15
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29
Consensus pattern (105 bp):
CTGATCTCTCCCCGGATCTCTGTGGACAACTCCTAGCATAATGATCCGTTTCTTTATAAATTAAA
CAAGCCCCATAGAACACTCTACAACTCCCCGATGAAATTT
Found at i:1109639 original size:54 final size:54
Alignment explanation
Indices: 1109579--1109990 Score: 412
Period size: 54 Copynumber: 7.6 Consensus size: 54
1109569 GTCATCCATA
* * * * * *
1109579 AACATATTATGAATTTTTTGATTTACACACATAGTGCCGAAACAGTTATTCATC
1 AACATATGATGAATTCTGTGAATTGCACACTTAGTGCCGAAACAGTTATTCATC
* * * * * *
1109633 AGCATATGATGAATTCTGTGAATTGCACACCTAGAGCCTATACGGTTATTCATC
1 AACATATGATGAATTCTGTGAATTGCACACTTAGTGCCGAAACAGTTATTCATC
* * * * * *** *
1109687 AACATATAACGAGTTATGTGAATTGCACACTTAATGTTTAAACGGTTATTCATC
1 AACATATGATGAATTCTGTGAATTGCACACTTAGTGCCGAAACAGTTATTCATC
* * * * * **
1109741 AACATATGATGCATTCCGTGAAGTGCACACGTAGTGTCGAAATGGTTATTCATC
1 AACATATGATGAATTCTGTGAATTGCACACTTAGTGCCGAAACAGTTATTCATC
* * * *
1109795 AACATATGATGAATTCTGTGAATTGCACATTTAGTTCTGAAACTGTTATTCATC
1 AACATATGATGAATTCTGTGAATTGCACACTTAGTGCCGAAACAGTTATTCATC
** *
1109849 AACATATGATGAATTCCATGAATTGCACACTTAGTG-CGAAACAATTATTCATC
1 AACATATGATGAATTCTGTGAATTGCACACTTAGTGCCGAAACAGTTATTCATC
* ** * * *
1109902 GACATATGATGAATTCCATGAATTGCACACTTAGTGGCGAAACAATTATTCATT
1 AACATATGATGAATTCTGTGAATTGCACACTTAGTGCCGAAACAGTTATTCATC
** * *
1109956 AACATATGATGAATTCCATGAAGTGAACACTTAGT
1 AACATATGATGAATTCTGTGAATTGCACACTTAGT
1109991 CCAATATAGG
Statistics
Matches: 301, Mismatches: 56, Indels: 2
0.84 0.16 0.01
Matches are distributed among these distances:
53 49 0.16
54 252 0.84
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (54 bp):
AACATATGATGAATTCTGTGAATTGCACACTTAGTGCCGAAACAGTTATTCATC
Found at i:1116547 original size:192 final size:192
Alignment explanation
Indices: 1116256--1116605 Score: 499
Period size: 192 Copynumber: 1.8 Consensus size: 192
1116246 CTTAAATAGG
* * * * *
1116256 TATTATTTTAATTTTAAATATACAAAATTATATAATTATATTTTATATTCAAAGTTAAAAAGGTA
1 TATTATTTTAATTTGAAATATACAAAAGTAAATAATTATATTTAATATTCAAAGTTAAAAAGATA
* * * * * *
1116321 ACAAATACATTTTTAAGTTTATATATTTAAAGAGTAATTTTACTACTAATATTTAAATTAAATAA
66 ACAAATACATTCTTAAATTGATATATTAAAAGAGTAATTATACTACTAATATTCAAATTAAA-AA
*
1116386 -T-TTATTTAATTTGCAACGGTCAAAAGGTAAACTCTTTTTACTATTCAAACTGAAAAACAAA
130 TTATTATTTAATTTGCAACAGTCAAAAGGTAAACTCTTTTTACTATTCAAACTGAAAAACAAA
* *
1116447 TATTATTTTAATTTGAAATATACAAAAGTAAATAGTTATCTTTGAATATTCAAAGTTAAAAAGAT
1 TATTATTTTAATTTGAAATATACAAAAGTAAATAATTATATTT-AATATTCAAAGTTAAAAAGAT
*
1116512 AACAAATACCTTCTTAAATTGACT-TATTAAAAGAGTAATTATACTACTAATATTCAAATTAAAA
65 AACAAATACATTCTTAAATTGA-TATATTAAAAGAGTAATTATACTACTAATATTCAAATTAAAA
* *
1116576 ATTATTTTTTAATTTGCAATAGTCAAAAGG
129 ATTATTATTTAATTTGCAACAGTCAAAAGG
1116606 ATTATGAATT
Statistics
Matches: 138, Mismatches: 17, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
191 40 0.29
192 74 0.54
193 24 0.17
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (192 bp):
TATTATTTTAATTTGAAATATACAAAAGTAAATAATTATATTTAATATTCAAAGTTAAAAAGATA
ACAAATACATTCTTAAATTGATATATTAAAAGAGTAATTATACTACTAATATTCAAATTAAAAAT
TATTATTTAATTTGCAACAGTCAAAAGGTAAACTCTTTTTACTATTCAAACTGAAAAACAAA
Found at i:1126088 original size:17 final size:16
Alignment explanation
Indices: 1126046--1126075 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1126036 CATATTTTAA
1126046 TTTAA-TTGTTTCTAG
1 TTTAATTTGTTTCTAG
1126061 TTTAATTTGTTTCTA
1 TTTAATTTGTTTCTA
1126076 ATTTTACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.07, G:0.10, T:0.63
Consensus pattern (16 bp):
TTTAATTTGTTTCTAG
Found at i:1132789 original size:17 final size:17
Alignment explanation
Indices: 1132769--1132805 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1132759 TGCTTAGCTA
*
1132769 GTTGACTAGCATTGCTG
1 GTTGACTAGCATTGATG
1132786 GTTGACTAGCATTGATG
1 GTTGACTAGCATTGATG
1132803 GTT
1 GTT
1132806 CCTTGATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.14, G:0.30, T:0.38
Consensus pattern (17 bp):
GTTGACTAGCATTGATG
Found at i:1140154 original size:14 final size:14
Alignment explanation
Indices: 1140135--1140166 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1140125 GAAAAAGACT
1140135 AAATAATATGGCTA
1 AAATAATATGGCTA
1140149 AAATAATATGGCTA
1 AAATAATATGGCTA
1140163 AAAT
1 AAAT
1140167 TCAAGGCAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.28
Consensus pattern (14 bp):
AAATAATATGGCTA
Found at i:1179453 original size:28 final size:28
Alignment explanation
Indices: 1179422--1179475 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
1179412 TATAGGTACC
*
1179422 TAAAAAATTAAAATAAAATTAA-AGTATA
1 TAAAAAACT-AAATAAAATTAACAGTATA
*
1179450 TAAAATACTAAATAAAATTAACAGTA
1 TAAAAAACTAAATAAAATTAACAGTA
1179476 AATTAAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.28
Consensus pattern (28 bp):
TAAAAAACTAAATAAAATTAACAGTATA
Found at i:1183638 original size:53 final size:53
Alignment explanation
Indices: 1183571--1183682 Score: 161
Period size: 53 Copynumber: 2.1 Consensus size: 53
1183561 CTATGTGTAC
* *
1183571 TTTCGACAGTATGTGTGCGCCCATGGTATTCATAATGAGTTTGTCAATTTCCA
1 TTTCGACAGTATGTGTGCACCCATGGAATTCATAATGAGTTTGTCAATTTCCA
* * * * *
1183624 TTTCGGCATTATGTGTGCATCCATGGAATTCATAATGATTTTGTGAATTTCCA
1 TTTCGACAGTATGTGTGCACCCATGGAATTCATAATGAGTTTGTCAATTTCCA
1183677 TTTCGA
1 TTTCGA
1183683 TACTTAGGTG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (53 bp):
TTTCGACAGTATGTGTGCACCCATGGAATTCATAATGAGTTTGTCAATTTCCA
Found at i:1192726 original size:13 final size:13
Alignment explanation
Indices: 1192673--1192728 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
1192663 CAATGCGTGC
*
1192673 CATAAATGCGCAT
1 CATAAATGCGCGT
* * *
1192686 AATAAATGAGTGT
1 CATAAATGCGCGT
*
1192699 CATAAATGTC-TGT
1 CATAAATG-CGCGT
1192712 CATAAATGCGCGT
1 CATAAATGCGCGT
1192725 CATA
1 CATA
1192729 GATTTATGAC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
12 1 0.03
13 33 0.97
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (13 bp):
CATAAATGCGCGT
Found at i:1199907 original size:23 final size:22
Alignment explanation
Indices: 1199854--1199958 Score: 97
Period size: 23 Copynumber: 4.8 Consensus size: 22
1199844 GAGTCGAGGG
** *
1199854 TTCTACGCAGTCCTTCGGGACA
1 TTCTACGTGGTCCTTCGGGAAA
*
1199876 -TCTATGTGGTCCTTCGGGAGAA
1 TTCTACGTGGTCCTTCGGGA-AA
*
1199898 TTCTACGTGGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGA-AA
* * *
1199921 TTCTACGCGGTCCTTTGGGACA
1 TTCTACGTGGTCCTTCGGGAAA
*
1199943 -TCTATGTGGTCCTTCG
1 TTCTACGTGGTCCTTCG
1199959 ACACATTTTA
Statistics
Matches: 67, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
21 29 0.43
22 1 0.01
23 37 0.55
ACGTcount: A:0.14, C:0.26, G:0.27, T:0.33
Consensus pattern (22 bp):
TTCTACGTGGTCCTTCGGGAAA
Found at i:1199952 original size:44 final size:44
Alignment explanation
Indices: 1199854--1199958 Score: 115
Period size: 44 Copynumber: 2.4 Consensus size: 44
1199844 GAGTCGAGGG
** * *
1199854 TTCTACGCAGTCCTTCGGGACATCTATGTGGTCCTTCGGGAGAA
1 TTCTACGTGGTCCTTCGGGACATCTACGCGGTCCTTCGGGAGAA
* *
1199898 TTCTACGTGGTCCTTCGGGACATTTCTACGCGGTCCTTTGGGA-CA
1 TTCTACGTGGTCCTTCGGGACA--TCTACGCGGTCCTTCGGGAGAA
*
1199943 -TCTATGTGGTCCTTCG
1 TTCTACGTGGTCCTTCG
1199959 ACACATTTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
44 35 0.67
45 1 0.02
46 16 0.31
ACGTcount: A:0.14, C:0.26, G:0.27, T:0.33
Consensus pattern (44 bp):
TTCTACGTGGTCCTTCGGGACATCTACGCGGTCCTTCGGGAGAA
Found at i:1202428 original size:15 final size:16
Alignment explanation
Indices: 1202410--1202442 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1202400 AAGAAAAACG
1202410 AAAAT-AAATGAATAA
1 AAAATAAAATGAATAA
1202425 AAAATAAAATGAATAA
1 AAAATAAAATGAATAA
1202441 AA
1 AA
1202443 TATAGTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (16 bp):
AAAATAAAATGAATAA
Found at i:1202463 original size:19 final size:17
Alignment explanation
Indices: 1202441--1202500 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
1202431 AAATGAATAA
1202441 AATATAGTAAATAATATAT
1 AATATA-TAAAT-ATATAT
1202460 AATATATAAATATATAT
1 AATATATAAATATATAT
* *
1202477 -AT-TTTAAAAACTATAT
1 AATATATAAATA-TATAT
1202493 AATATATA
1 AATATATA
1202501 TATTTTCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
15 6 0.17
16 7 0.20
17 8 0.23
18 8 0.23
19 6 0.17
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
AATATATAAATATATAT
Found at i:1202499 original size:25 final size:26
Alignment explanation
Indices: 1202462--1202530 Score: 113
Period size: 26 Copynumber: 2.7 Consensus size: 26
1202452 TAATATATAA
1202462 TATATAAATATATATATTTT-AAAAAC
1 TATAT-AATATATATATTTTCAAAAAC
1202488 TATATAATATATATATTTTCAAAAAC
1 TATATAATATATATATTTTCAAAAAC
*
1202514 TATATATTATATATATT
1 TATATAATATATATATT
1202531 CAAAATGTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 14 0.34
26 27 0.66
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.46
Consensus pattern (26 bp):
TATATAATATATATATTTTCAAAAAC
Found at i:1202529 original size:37 final size:37
Alignment explanation
Indices: 1202500--1202781 Score: 261
Period size: 39 Copynumber: 7.7 Consensus size: 37
1202490 TATAATATAT
1202500 ATATTTTCAAAAACTATATATTATATATA--TTCAAA
1 ATATTTTCAAAAACTATATATTATATATATTTTCAAA
* *
1202535 ATGTTTTCAAAAACTATATATTATATATATTTTCAAT
1 ATATTTTCAAAAACTATATATTATATATATTTTCAAA
*
1202572 ATGTTTTCAAAAAC--TATA-TATA-ATA---T----
1 ATATTTTCAAAAACTATATATTATATATATTTTCAAA
*
1202598 ATATTTTCAAAAACTATATATTATATATATGTTTTTAAA
1 ATATTTTCAAAAACTATATATTATATATA--TTTTCAAA
*
1202637 ATGTTTTCAAAAACTATATATTATATATATTTTCAAA
1 ATATTTTCAAAAACTATATATTATATATATTTTCAAA
* *
1202674 ATATTTT-TAAAACTATATATCATATATATGTTTTCAAAA
1 ATATTTTCAAAAACTATATAT--TATATATATTTTC-AAA
* * *
1202713 CATCTTTTTTAAAAAACTATATATTGTATATACGTTTTCAAA
1 -A--TATTTTCAAAAACTATATATTATATATA--TTTTCAAA
*
1202755 AT-TTTATAAAAAACTATATATTATATA
1 ATATTT-TCAAAAACTATATATTATATA
1202782 CTTTATATAT
Statistics
Matches: 209, Mismatches: 13, Indels: 46
0.78 0.05 0.17
Matches are distributed among these distances:
26 13 0.06
28 4 0.02
29 4 0.02
30 4 0.02
33 3 0.01
34 4 0.02
35 33 0.16
36 12 0.06
37 32 0.15
38 15 0.07
39 52 0.25
40 1 0.00
41 7 0.03
42 8 0.04
43 17 0.08
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (37 bp):
ATATTTTCAAAAACTATATATTATATATATTTTCAAA
Found at i:1202601 original size:28 final size:28
Alignment explanation
Indices: 1202570--1202637 Score: 104
Period size: 26 Copynumber: 2.5 Consensus size: 28
1202560 TATATTTTCA
1202570 ATATGTTTTCAAAAACTATATATAATAT
1 ATATGTTTTCAAAAACTATATATAATAT
*
1202598 ATA--TTTTCAAAAACTATATATTATAT
1 ATATGTTTTCAAAAACTATATATAATAT
*
1202624 ATATGTTTTTAAAA
1 ATATGTTTTCAAAA
1202638 TGTTTTCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
26 25 0.69
28 11 0.31
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (28 bp):
ATATGTTTTCAAAAACTATATATAATAT
Found at i:1202625 original size:65 final size:63
Alignment explanation
Indices: 1202461--1202674 Score: 231
Period size: 65 Copynumber: 3.4 Consensus size: 63
1202451 ATAATATATA
* * ** * **
1202461 ATATATAAATATATATATTTTAAAAACTATATAATATATATATTTTCAAAA-ACTAT-ATATTA-
1 ATATAT-AATATATAT-TTTCAAAAACTATATATTATATATATTTTCAAAATGTTTTCA-AAAAC
1202523 T
63 T
* *
1202524 ATATATTCAA-A-ATGTTTTCAAAAACTATATATTATATATATTTTCAATATGTTTTCAAAAACT
1 ATATA-T-AATATATATTTTCAAAAACTATATATTATATATATTTTCAAAATGTTTTCAAAAACT
*
1202587 ATATATAATATATATTTTCAAAAACTATATATTATATATATGTTTTTAAAATGTTTTCAAAAACT
1 ATATATAATATATATTTTCAAAAACTATATATTATATATA--TTTTCAAAATGTTTTCAAAAACT
*
1202652 ATATATTATATATATTTTCAAAA
1 ATATATAATATATATTTTCAAAA
1202675 TATTTTTAAA
Statistics
Matches: 129, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
61 33 0.26
62 9 0.07
63 41 0.32
64 3 0.02
65 43 0.33
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (63 bp):
ATATATAATATATATTTTCAAAAACTATATATTATATATATTTTCAAAATGTTTTCAAAAACT
Found at i:1205066 original size:44 final size:44
Alignment explanation
Indices: 1205018--1205140 Score: 183
Period size: 44 Copynumber: 2.8 Consensus size: 44
1205008 ATATGAGAAC
* *
1205018 AAGATATAAGTTATGTGACATGATCTACATGATTACATGAACAT
1 AAGATATAAGATATGTGACATGATCTACGTGATTACATGAACAT
* *
1205062 AAGATATAAGATGTGTGACATGATCTACGTGATTACATGAACGT
1 AAGATATAAGATATGTGACATGATCTACGTGATTACATGAACAT
* * *
1205106 AAGATATAAGCTATGTGACATAACCTACGTGATTA
1 AAGATATAAGATATGTGACATGATCTACGTGATTA
1205141 TTGGTCTTTT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 71 1.00
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (44 bp):
AAGATATAAGATATGTGACATGATCTACGTGATTACATGAACAT
Found at i:1205279 original size:23 final size:22
Alignment explanation
Indices: 1205223--1205324 Score: 93
Period size: 23 Copynumber: 4.6 Consensus size: 22
1205213 GGGTATAGGG
* *
1205223 TTCTACATGGTCCTTCGGGACA
1 TTCTACGTGGTCCTTCGAGACA
* *
1205245 -TCTATGTTGTCCTTCGAGACAA
1 TTCTACGTGGTCCTTCGAGAC-A
1205267 TTCTACGTGGTCCTTC-AGGACA
1 TTCTACGTGGTCCTTCGA-GACA
* *
1205289 TTTCTACGTAGTCCTTCGGGACA
1 -TTCTACGTGGTCCTTCGAGACA
*
1205312 -TCTATGTGGTCCT
1 TTCTACGTGGTCCT
1205325 ATGTGACACT
Statistics
Matches: 65, Mismatches: 10, Indels: 11
0.76 0.12 0.13
Matches are distributed among these distances:
21 27 0.42
22 3 0.05
23 35 0.54
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (22 bp):
TTCTACGTGGTCCTTCGAGACA
Found at i:1205288 original size:44 final size:44
Alignment explanation
Indices: 1205223--1205324 Score: 118
Period size: 44 Copynumber: 2.3 Consensus size: 44
1205213 GGGTATAGGG
* * * *
1205223 TTCTACATGGTCCTTCGGGACA-TCTATGTTGTCCTTCGAGACAA
1 TTCTACGTGGTCCTTCAGGACATTCTACGTAGTCCTTCGAGAC-A
*
1205267 TTCTACGTGGTCCTTCAGGACATTTCTACGTAGTCCTTCGGGACA
1 TTCTACGTGGTCCTTCAGGACA-TTCTACGTAGTCCTTCGAGACA
*
1205312 -TCTATGTGGTCCT
1 TTCTACGTGGTCCT
1205325 ATGTGACACT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
44 32 0.64
45 1 0.02
46 17 0.34
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (44 bp):
TTCTACGTGGTCCTTCAGGACATTCTACGTAGTCCTTCGAGACA
Found at i:1207450 original size:17 final size:18
Alignment explanation
Indices: 1207430--1207477 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
1207420 CTGAAATATA
*
1207430 AAAATAAAATAAATT-TT
1 AAAATAAAATAAATTATG
1207447 AAAAT-AAATAAAATTATG
1 AAAATAAAAT-AAATTATG
1207465 AAAATAAAATAAA
1 AAAATAAAATAAA
1207478 ATAAAAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 4 0.15
17 10 0.37
18 9 0.33
19 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (18 bp):
AAAATAAAATAAATTATG
Found at i:1213759 original size:54 final size:54
Alignment explanation
Indices: 1213691--1214343 Score: 837
Period size: 54 Copynumber: 12.1 Consensus size: 54
1213681 ACATAAGTAC
* * *
1213691 CGATATGGAAATTCACAAACTCATTATGAATTACATGGGTTGCACACATAGTGC
1 CGATACGGTAATTCACAAACTCATTATGAATTACATGGGTTGCACACATAGTGT
** * * *
1213745 CGATATAGTAATTCACAAACTTATTTTGAATTCCATGGGTTGCACACATAGTGT
1 CGATACGGTAATTCACAAACTCATTATGAATTACATGGGTTGCACACATAGTGT
* **
1213799 CGATACGGTAATTCATAAACTCATTATGAATTATGTGGGTTGCACACATAGTGT
1 CGATACGGTAATTCACAAACTCATTATGAATTACATGGGTTGCACACATAGTGT
** * * *
1213853 CGATACGACAATTCACAAACTCATTATGACTTACATGGGTTGCACATATAGTAT
1 CGATACGGTAATTCACAAACTCATTATGAATTACATGGGTTGCACACATAGTGT
* ***
1213907 CGATATGGTAATTCACAAACTCATTATGAATTTTGTGGGTTGCACACATAGTGT
1 CGATACGGTAATTCACAAACTCATTATGAATTACATGGGTTGCACACATAGTGT
* * ***
1213961 CGATACTGTAATTCACAAACTCAATATGAATTTTGTGGGTTGCACACATAGTGT
1 CGATACGGTAATTCACAAACTCATTATGAATTACATGGGTTGCACACATAGTGT
* *** *
1214015 CAATACGGTAATTCACAAACTCATTATGAATTTTGTGGGTTGCACACATAGTGC
1 CGATACGGTAATTCACAAACTCATTATGAATTACATGGGTTGCACACATAGTGT
*
1214069 CGATACGGTAATTCAAAAACTCATTATGAATT-CTATGGGTTGCACACATAGTG-
1 CGATACGGTAATTCACAAACTCATTATGAATTAC-ATGGGTTGCACACATAGTGT
* *
1214122 CTGATACTGTAATTCACAAACTCATTATGAATT-CTGTGGGTTGCACACATAGTGT
1 C-GATACGGTAATTCACAAACTCATTATGAATTAC-ATGGGTTGCACACATAGTGT
*** **
1214177 CGATACGGTAATTCACAAACTCATTATGAATTTTGTGGGTTGCACACATAGTAC
1 CGATACGGTAATTCACAAACTCATTATGAATTACATGGGTTGCACACATAGTGT
* * * * *
1214231 CAATACGGTAATTCACAAACTCATTATGAGTTATATGGGTTACACACATAGTGC
1 CGATACGGTAATTCACAAACTCATTATGAATTACATGGGTTGCACACATAGTGT
* *
1214285 CGATACGGTAATTCACAAACTCGTTATGAATT-CAATGGGTTGAACACATAGTGT
1 CGATACGGTAATTCACAAACTCATTATGAATTAC-ATGGGTTGCACACATAGTGT
1214339 CGATA
1 CGATA
1214344 GTACACATAG
Statistics
Matches: 532, Mismatches: 62, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
53 1 0.00
54 530 1.00
55 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Consensus pattern (54 bp):
CGATACGGTAATTCACAAACTCATTATGAATTACATGGGTTGCACACATAGTGT
Found at i:1213974 original size:162 final size:162
Alignment explanation
Indices: 1213691--1214343 Score: 923
Period size: 162 Copynumber: 4.0 Consensus size: 162
1213681 ACATAAGTAC
* * * **
1213691 CGATATGGAAATTCACAAACTCATTATGAATTACATGGGTTGCACACATAGTGCCGATATAGTAA
1 CGATACGGTAATTCACAAACTCATTATGAATTACATGGGTTGCACACATAGTACCGATACGGTAA
* * * *
1213756 TTCACAAACTTATTTTGAATTCCATGGGTTGCACACATAGTGTCGATACGGTAATTCATAAACTC
66 TTCACAAACTCATTATGAATTCTATGGGTTGCACACATAGTGTCGATACGGTAATTCACAAACTC
1213821 ATTATGAATTATGTGGGTTGCACACATAGTGT
131 ATTATGAATTATGTGGGTTGCACACATAGTGT
** * * * *
1213853 CGATACGACAATTCACAAACTCATTATGACTTACATGGGTTGCACATATAGTATCGATATGGTAA
1 CGATACGGTAATTCACAAACTCATTATGAATTACATGGGTTGCACACATAGTACCGATACGGTAA
* * *
1213918 TTCACAAACTCATTATGAATTTTGTGGGTTGCACACATAGTGTCGATACTGTAATTCACAAACTC
66 TTCACAAACTCATTATGAATTCTATGGGTTGCACACATAGTGTCGATACGGTAATTCACAAACTC
* *
1213983 AATATGAATTTTGTGGGTTGCACACATAGTGT
131 ATTATGAATTATGTGGGTTGCACACATAGTGT
* *** *
1214015 CAATACGGTAATTCACAAACTCATTATGAATTTTGTGGGTTGCACACATAGTGCCGATACGGTAA
1 CGATACGGTAATTCACAAACTCATTATGAATTACATGGGTTGCACACATAGTACCGATACGGTAA
* *
1214080 TTCAAAAACTCATTATGAATTCTATGGGTTGCACACATAGTG-CTGATACTGTAATTCACAAACT
66 TTCACAAACTCATTATGAATTCTATGGGTTGCACACATAGTGTC-GATACGGTAATTCACAAACT
*
1214144 CATTATGAATTCTGTGGGTTGCACACATAGTGT
130 CATTATGAATTATGTGGGTTGCACACATAGTGT
*** *
1214177 CGATACGGTAATTCACAAACTCATTATGAATTTTGTGGGTTGCACACATAGTACCAATACGGTAA
1 CGATACGGTAATTCACAAACTCATTATGAATTACATGGGTTGCACACATAGTACCGATACGGTAA
* * * *
1214242 TTCACAAACTCATTATGAGTTATATGGGTTACACACATAGTGCCGATACGGTAATTCACAAACTC
66 TTCACAAACTCATTATGAATTCTATGGGTTGCACACATAGTGTCGATACGGTAATTCACAAACTC
* * *
1214307 GTTATGAATTCA-ATGGGTTGAACACATAGTGT
131 ATTATGAATT-ATGTGGGTTGCACACATAGTGT
1214339 CGATA
1 CGATA
1214344 GTACACATAG
Statistics
Matches: 443, Mismatches: 45, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
161 1 0.00
162 441 1.00
163 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Consensus pattern (162 bp):
CGATACGGTAATTCACAAACTCATTATGAATTACATGGGTTGCACACATAGTACCGATACGGTAA
TTCACAAACTCATTATGAATTCTATGGGTTGCACACATAGTGTCGATACGGTAATTCACAAACTC
ATTATGAATTATGTGGGTTGCACACATAGTGT
Found at i:1215554 original size:13 final size:13
Alignment explanation
Indices: 1215536--1215563 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1215526 CTTCAAAACC
1215536 AACCCATAAGCGA
1 AACCCATAAGCGA
1215549 AACCCATAAGCGA
1 AACCCATAAGCGA
1215562 AA
1 AA
1215564 GGAAAAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.29, G:0.14, T:0.07
Consensus pattern (13 bp):
AACCCATAAGCGA
Found at i:1217286 original size:2 final size:2
Alignment explanation
Indices: 1217281--1217327 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
1217271 AAAAATATGA
1217281 AT AT AT AT AT AT -T AT AT AT AT AT -T 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
1217321 -T AT AT AT
1 AT AT AT AT
1217328 CTTATATGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.07
2 39 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1217298 original size:11 final size:11
Alignment explanation
Indices: 1217282--1217327 Score: 74
Period size: 11 Copynumber: 4.0 Consensus size: 11
1217272 AAAATATGAA
1217282 TATATATATAT
1 TATATATATAT
1217293 TATATATATAT
1 TATATATATAT
1217304 TATATATATAT
1 TATATATATAT
1217315 ATATATTATATAT
1 -TATA-TATATAT
1217328 CTTATATGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 22 0.67
12 4 0.12
13 7 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TATATATATAT
Found at i:1217299 original size:13 final size:13
Alignment explanation
Indices: 1217281--1217327 Score: 76
Period size: 13 Copynumber: 3.5 Consensus size: 13
1217271 AAAAATATGA
1217281 ATATATATATATT
1 ATATATATATATT
1217294 ATATATATATTATAT
1 ATATATATA-TAT-T
1217309 ATATATATATATT
1 ATATATATATATT
1217322 ATATAT
1 ATATAT
1217328 CTTATATGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
13 16 0.50
14 6 0.19
15 10 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATATATATATATT
Found at i:1217317 original size:26 final size:26
Alignment explanation
Indices: 1217281--1217334 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
1217271 AAAAATATGA
1217281 ATATATATATAT-TA-TATATATATT
1 ATATATATATATATATTATATATATT
*
1217305 ATATATATATATATATTATATATCTT
1 ATATATATATATATATTATATATATT
1217331 ATAT
1 ATAT
1217335 GATTAGAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 12 0.44
25 2 0.07
26 13 0.48
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (26 bp):
ATATATATATATATATTATATATATT
Found at i:1217339 original size:17 final size:17
Alignment explanation
Indices: 1217281--1217327 Score: 80
Period size: 17 Copynumber: 2.9 Consensus size: 17
1217271 AAAAATATGA
1217281 ATATATA-TATAT-TAT
1 ATATATATTATATATAT
1217296 ATATATATTATATATAT
1 ATATATATTATATATAT
1217313 ATATATATTATATAT
1 ATATATATTATATAT
1217328 CTTATATGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.23
16 5 0.17
17 18 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATATATTATATATAT
Found at i:1232902 original size:161 final size:160
Alignment explanation
Indices: 1232664--1233003 Score: 361
Period size: 161 Copynumber: 2.1 Consensus size: 160
1232654 GAATTGGGTG
* ** * * *
1232664 AAGGTTGAACAAGTCCTTC-TGATTATTCACTTCTTCTCTTAGAAATGTTGATCCACCTCTTTTT
1 AAGGTTGAACAAGTTCTTCTTGATTATGAACTTCTTCTCTTAGAAATGATGATCCACCTCATTCT
* * ** * *
1232728 GTGTTGAAATTGAGCAAAGTTTTCAACAAGTTCTT-T-TAATTTTGAACTT-TTCCTCTCATAAA
66 ATGTTGAAATTGAGCAAAG-GTTCAACAAGTTCTTCTCTAATAATGAACTTATT-CTATCAGAAA
* * *
1232790 TGCTGATCCAACTCTTTTTATGATGGAATCGAGCA
129 AGATGATCCAACTC--CTTAT-ATGGAATCGAGCA
* *
1232825 AAGGTTGAACAAGTTCTTCTTG-TTATGAACTTCTTCTCTTGGAAATGATG-TCCTATCTCATTC
1 AAGGTTGAACAAGTTCTTCTTGATTATGAACTTCTTCTCTTAGAAATGATGATCC-ACCTCATTC
* * * *
1232888 TAT-TATGCAATTGAGCAAAGGTTGAACAAGTTCTTCTCTCATAATGAACTTATTCTATTAGAAA
65 TATGT-TGAAATTGAGCAAAGGTTCAACAAGTTCTTCTCTAATAATGAACTTATTCTATCAGAAA
*
1232952 AGATGATCCAACTCCTTCTATGGAATCGAGCA
129 AGATGATCCAACTCCTTATATGGAATCGAGCA
*
1232984 AAGGTTGACCAAGTTCTTCT
1 AAGGTTGAACAAGTTCTTCT
1233004 CATTATAAAT
Statistics
Matches: 150, Mismatches: 23, Indels: 14
0.80 0.12 0.07
Matches are distributed among these distances:
159 32 0.21
160 20 0.13
161 65 0.43
162 31 0.21
163 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (160 bp):
AAGGTTGAACAAGTTCTTCTTGATTATGAACTTCTTCTCTTAGAAATGATGATCCACCTCATTCT
ATGTTGAAATTGAGCAAAGGTTCAACAAGTTCTTCTCTAATAATGAACTTATTCTATCAGAAAAG
ATGATCCAACTCCTTATATGGAATCGAGCA
Found at i:1233004 original size:79 final size:79
Alignment explanation
Indices: 1232812--1233004 Score: 230
Period size: 79 Copynumber: 2.4 Consensus size: 79
1232802 TCTTTTTATG
* * * * * *
1232812 ATGGAATCGAGCAAAGGTTGAACAAGTTCTTCT-TGTTATGAACTTCTTCTCTTGGAAATGATGT
1 ATGGAATCGAGCAAAGGTTGAACAAGTTCTTCTCTATAATGAACTTATTCTATTAGAAAAGATGT
*
1232876 CCTATCTCATTCTATT
66 CCTAACTCATTC--TT
* *
1232892 ATGCAATTGAGCAAAGGTTGAACAAGTTCTTCTCTCATAATGAACTTATTCTATTAGAAAAGATG
1 ATGGAATCGAGCAAAGGTTGAACAAGTTCTTCTCT-ATAATGAACTTATTCTATTAGAAAAGATG
*
1232957 ATCC-AACTCCTTC-T
65 -TCCTAACTCATTCTT
*
1232971 ATGGAATCGAGCAAAGGTTGACCAAGTTCTTCTC
1 ATGGAATCGAGCAAAGGTTGAACAAGTTCTTCTC
1233005 ATTATAAATT
Statistics
Matches: 97, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
79 32 0.33
80 31 0.32
81 1 0.01
82 30 0.31
83 3 0.03
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (79 bp):
ATGGAATCGAGCAAAGGTTGAACAAGTTCTTCTCTATAATGAACTTATTCTATTAGAAAAGATGT
CCTAACTCATTCTT
Found at i:1240305 original size:21 final size:21
Alignment explanation
Indices: 1240276--1240318 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1240266 TTATTATTGC
*
1240276 AAGAATTCATGGCCTCGACAA
1 AAGAATTCATGGCCTCCACAA
* *
1240297 AAGATTTCATGGCTTCCACAA
1 AAGAATTCATGGCCTCCACAA
1240318 A
1 A
1240319 GACCTTGATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.23
Consensus pattern (21 bp):
AAGAATTCATGGCCTCCACAA
Found at i:1241316 original size:13 final size:13
Alignment explanation
Indices: 1241298--1241327 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1241288 CAGTCACGGG
1241298 ATGGCGCATATGC
1 ATGGCGCATATGC
*
1241311 ATGGCGCATATTC
1 ATGGCGCATATGC
1241324 ATGG
1 ATGG
1241328 ATTATCGGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (13 bp):
ATGGCGCATATGC
Found at i:1250742 original size:29 final size:30
Alignment explanation
Indices: 1250687--1250743 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
1250677 TTTTGTCCCT
* *
1250687 AAACTTTTACAACTTTATATTATGGTCAAC
1 AAACTTTCAAAACTTTATATTATGGTCAAC
*
1250717 AAACTTTCAAAAC-TTATATTTTGGTCA
1 AAACTTTCAAAACTTTATATTATGGTCA
1250744 TTTAAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.40
Consensus pattern (30 bp):
AAACTTTCAAAACTTTATATTATGGTCAAC
Found at i:1252778 original size:66 final size:68
Alignment explanation
Indices: 1252701--1252828 Score: 206
Period size: 66 Copynumber: 1.9 Consensus size: 68
1252691 TCAAAGGCAT
* *
1252701 TTAACCTTTCATCTAACTGCCAT-GTTGACACTTTTATGTCAAATGCA-AGTTAGGCCTCAAGAG
1 TTAACCTTTCATCTAACTGCCATAATTGACACCTTTATGTCAAATGCATAGTTAGGCCTCAAGAG
1252764 CAC
66 CAC
* *
1252767 TTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCATAGTTAGGCCTCAA
1 TTAACCTTTCATCTAACTGCCATAATTGACACCTTTATGTCAAATGCATAGTTAGGCCTCAA
1252829 ATCTTTTATT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
66 22 0.39
67 21 0.38
68 13 0.23
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (68 bp):
TTAACCTTTCATCTAACTGCCATAATTGACACCTTTATGTCAAATGCATAGTTAGGCCTCAAGAG
CAC
Found at i:1253175 original size:59 final size:59
Alignment explanation
Indices: 1253103--1253243 Score: 266
Period size: 59 Copynumber: 2.4 Consensus size: 59
1253093 AACATTACCC
1253103 ATATGGAAATTCATACACTTAGTATGAATTCCTTAACAGTTTAGCACACGAAGTGCCCT
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTAACAGTTTAGCACACGAAGTGCCCT
*
1253162 ATATGGAAATTCATACACTTAGTATGAATTCCTTAACAGTTTAGCACACGATGTGCCCT
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTAACAGTTTAGCACACGAAGTGCCCT
1253221 ATATGGAAATTCATAC-CTTAGTA
1 ATATGGAAATTCATACACTTAGTA
1253244 CCTATCTAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
58 7 0.09
59 74 0.91
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (59 bp):
ATATGGAAATTCATACACTTAGTATGAATTCCTTAACAGTTTAGCACACGAAGTGCCCT
Found at i:1253304 original size:85 final size:86
Alignment explanation
Indices: 1253167--1253326 Score: 259
Period size: 85 Copynumber: 1.9 Consensus size: 86
1253157 GCCCTATATG
**
1253167 GAAATTCATACACTTAGTATGAATTCCTTAACAGTTTAGCACACGATGTGCCCTATATGGAAATT
1 GAAATTCATACACTTAGTATGAATTCCTTAACAGTTTAGCACACGAAATGCCCTATATGGAAATT
1253232 CATAC-CTTAGTACCTATCTA
66 CATACACTTAGTACCTATCTA
* * * *
1253252 GAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAATGCCCTATCTGGAAATT
1 GAAATTCATACACTTAGTATGAATTCCTTAACAGTTTAGCACACGAAATGCCCTATATGGAAATT
1253317 CATACACTTA
66 CATACACTTA
1253327 ATATGATTTC
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
85 64 0.94
86 4 0.06
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (86 bp):
GAAATTCATACACTTAGTATGAATTCCTTAACAGTTTAGCACACGAAATGCCCTATATGGAAATT
CATACACTTAGTACCTATCTA
Found at i:1253375 original size:144 final size:145
Alignment explanation
Indices: 1253108--1253388 Score: 438
Period size: 144 Copynumber: 1.9 Consensus size: 145
1253098 TACCCATATG
*
1253108 GAAATTCATACACTTAGTATGAATTCCTTAACAGTTTAGCACACGAAGTGCCCTATATGGAAATT
1 GAAATTCATACACTTAGTATGAATTCCTTAACAGTTTAGCACACGAAATGCCCTATATGGAAATT
* * *
1253173 CATACACTTAGTATGAATTCCTTAACAGTTTAGCACACGATGTGCCCTATATGGAAATTCATAC-
66 CATACACTTAATATGAATTCCTTAACAGTTTAGCACACGAAGTGCCCTATATGAAAATTCATACA
1253237 CTTAGTACCTATCTA
131 CTTAGTACCTATCTA
* * * *
1253252 GAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAATGCCCTATCTGGAAATT
1 GAAATTCATACACTTAGTATGAATTCCTTAACAGTTTAGCACACGAAATGCCCTATATGGAAATT
* * * * *
1253317 CATACACTTAATATGATTTCCTTACCATTTTAGTACACGAAGTGCCCTATCTGAAAATTCATACA
66 CATACACTTAATATGAATTCCTTAACAGTTTAGCACACGAAGTGCCCTATATGAAAATTCATACA
1253382 CTTAGTA
131 CTTAGTA
1253389 TGATTTCCTT
Statistics
Matches: 123, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
144 116 0.94
145 7 0.06
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (145 bp):
GAAATTCATACACTTAGTATGAATTCCTTAACAGTTTAGCACACGAAATGCCCTATATGGAAATT
CATACACTTAATATGAATTCCTTAACAGTTTAGCACACGAAGTGCCCTATATGAAAATTCATACA
CTTAGTACCTATCTA
Found at i:1253499 original size:59 final size:59
Alignment explanation
Indices: 1253244--1253472 Score: 404
Period size: 59 Copynumber: 3.9 Consensus size: 59
1253234 TACCTTAGTA
* *
1253244 CCTATCTAGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAATGC
1 CCTATCTGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGC
* *
1253303 CCTATCTGGAAATTCATACACTTAATATGATTTCCTTACCATTTTAGTACACGAAGTGC
1 CCTATCTGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGC
*
1253362 CCTATCTGAAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGC
1 CCTATCTGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGC
*
1253421 TCTATCTGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACAC
1 CCTATCTGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACAC
1253473 TTAGTGTCAT
Statistics
Matches: 161, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 161 1.00
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (59 bp):
CCTATCTGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGC
Found at i:1254014 original size:94 final size:94
Alignment explanation
Indices: 1253853--1254025 Score: 238
Period size: 94 Copynumber: 1.8 Consensus size: 94
1253843 GGGTATCGAT
* * * *
1253853 ACCCCCTTCCACTATCGATACCAATTTTAGGTTTGATGTTGCCTAGTATTGATACCCTAACCGTG
1 ACCCCCTTCCACTATCGATACCAATTTTAGATTCGATGTTGCCTAGTATCGATACCCTAACCATG
*
1253918 GTATCGATACTACCATATTATGGTACTGA
66 GTATCAATACTACCATATTATGGTACTGA
* * * * * *
1253947 ACCCCCTTCCAGTATCGATACCCATTTTAGATTCGATGTTGCTTGGTATCGATACCCTTATCATG
1 ACCCCCTTCCACTATCGATACCAATTTTAGATTCGATGTTGCCTAGTATCGATACCCTAACCATG
*
1254012 GTATTAATACTACC
66 GTATCAATACTACC
1254026 TCTTCGGTAT
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
94 67 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (94 bp):
ACCCCCTTCCACTATCGATACCAATTTTAGATTCGATGTTGCCTAGTATCGATACCCTAACCATG
GTATCAATACTACCATATTATGGTACTGA
Found at i:1258720 original size:59 final size:59
Alignment explanation
Indices: 1258631--1259145 Score: 714
Period size: 59 Copynumber: 8.8 Consensus size: 59
1258621 ATTTCCCATA
* * * * * * *
1258631 TGGAAATTCATACACTTAGTATAAATTCCTTAACAATTTAGCACGCGAAGTGCCTTATA
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGCCCTATC
* * * * *
1258690 TGGAAATTCATACACTTAGTATGAATTCCTTAACAGTTTAGCACATGAAGTGCCCTATA
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGCCCTATC
* * * * *
1258749 TGGAAATGCATACACTTAGTATGAATTT-CTTAACAGTTTAGCACACGAAGTTCCCTATA
1 TGGAAATTCATACACTTAGTATG-ATTTCCTTACCATTTTAGCACACGAAGTGCCCTATC
*
1258808 TGGAAATTCATACACTTAGTATGATTTTCTTACCATTTTAG--CACGAAGTGCCCTATC
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGCCCTATC
* *
1258865 TGGAAATTCATACACTTAGTATGATATGCTTACCATTTTAGCACACGAAGTGCCCTATC
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGCCCTATC
* *
1258924 TGGAAATTCATACACTTAGTATGATTTCCTTGCCATTTTGGCACACGAAGTGCCCTATC
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGCCCTATC
* * *
1258983 TGGAAATTCTTACTCTTAGTATGATTTCTTTACCATTTTAGCACACGAAGTGCCCTATC
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGCCCTATC
* * *
1259042 T-AAAATTAATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGCCTTATC
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGCCCTATC
* * *
1259100 TGGAAATTAATACGCTTAGTATGATTTCCTAACCATTTTAGCACAC
1 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACAC
1259146 TTAGTGTCAT
Statistics
Matches: 417, Mismatches: 34, Indels: 10
0.90 0.07 0.02
Matches are distributed among these distances:
57 53 0.13
58 56 0.13
59 305 0.73
60 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (59 bp):
TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGCCCTATC
Found at i:1258921 original size:175 final size:173
Alignment explanation
Indices: 1258623--1259145 Score: 683
Period size: 175 Copynumber: 3.0 Consensus size: 173
1258613 ATACTCACAT
* * * * *
1258623 TTCCC-ATATGGAAATTCATACACTTAGTATAAATTCCTTAACAATTTAGCACGCGAAGTGCCTT
1 TTCCCTATATGGAAATTCATACACTTAGTAT-GATTTCTTACCATTTTAGCA--CGAAGTGCCCT
* * * * *
1258687 ATATGGAAATTCATACACTTAGTATGA-ATTCCTTAACAGTTTAGCACATGAAGTGCCCTATATG
63 ATCTGGAAATTCATACACTTAGTATGATA-TCCTTACCATTTTAGCACACGAAGTGCCCTATCTG
* *
1258751 GAAATGCATACACTTAGTATGAATTTCTTAACAGTTTAGCACACGAAG
127 GAAATTCATACACTTAGTATG-ATTTCTTAACATTTTAGCACACGAAG
1258799 TTCCCTATATGGAAATTCATACACTTAGTATGATTTTCTTACCATTTTAGCACGAAGTGCCCTAT
1 TTCCCTATATGGAAATTCATACACTTAGTATGA-TTTCTTACCATTTTAGCACGAAGTGCCCTAT
*
1258864 CTGGAAATTCATACACTTAGTATGATATGCTTACCATTTTAGCACACGAAGTGCCCTATCTGGAA
65 CTGGAAATTCATACACTTAGTATGATATCCTTACCATTTTAGCACACGAAGTGCCCTATCTGGAA
** *
1258929 ATTCATACACTTAGTATGATTTCCTTGCCATTTTGGCACACGAAG
130 ATTCATACACTTAGTATGATTT-CTTAACATTTTAGCACACGAAG
* * * *
1258974 TGCCCTATCTGGAAATTCTTACTCTTAGTATGATTTCTTTACCATTTTAGCACACGAAGTGCCCT
1 TTCCCTATATGGAAATTCATACACTTAGTATGATTTC-TTACCATTTTAG--CACGAAGTGCCCT
* * * *
1259039 ATCT-AAAATTAATACACTTAGTATGATTTCCTTACCATTTTAGCACACGAAGTGCCTTATCTGG
63 ATCTGGAAATTCATACACTTAGTATGATATCCTTACCATTTTAGCACACGAAGTGCCCTATCTGG
* * *
1259103 AAATTAATACGCTTAGTATGATTTCCTAACCATTTTAGCACAC
128 AAATTCATACACTTAGTATGATTTCTTAA-CATTTTAGCACAC
1259146 TTAGTGTCAT
Statistics
Matches: 308, Mismatches: 31, Indels: 16
0.87 0.09 0.05
Matches are distributed among these distances:
174 8 0.03
175 147 0.48
176 96 0.31
177 57 0.19
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (173 bp):
TTCCCTATATGGAAATTCATACACTTAGTATGATTTCTTACCATTTTAGCACGAAGTGCCCTATC
TGGAAATTCATACACTTAGTATGATATCCTTACCATTTTAGCACACGAAGTGCCCTATCTGGAAA
TTCATACACTTAGTATGATTTCTTAACATTTTAGCACACGAAG
Found at i:1259658 original size:94 final size:95
Alignment explanation
Indices: 1259518--1259698 Score: 265
Period size: 94 Copynumber: 1.9 Consensus size: 95
1259508 CTGTACTAGG
*
1259518 GTATCGATATCCCCTTCCACTATCGATACCAAATTTAGGTTCGATGTTGCCTAGTATCGATACCC
1 GTATCGATATCCCCTTCCACTATCGATACCAAATTTAGATTCGATGTTGCCTAGTATCGATACCC
*
1259583 TTACCATGGTATCGATACTACCATAGTATA
66 TTACCATGGCATCGATACTACCATAGTATA
* * * * * * *
1259613 GTATTGATA-CCCCTTCCAGTATCGATACCCATTTTAGATTTGATGTTGCTTGGTATCGATACCC
1 GTATCGATATCCCCTTCCACTATCGATACCAAATTTAGATTCGATGTTGCCTAGTATCGATACCC
*
1259677 TTATCATGGCATCGATACTACC
66 TTACCATGGCATCGATACTACC
1259699 TCTTCGATAT
Statistics
Matches: 76, Mismatches: 10, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
94 68 0.89
95 8 0.11
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.34
Consensus pattern (95 bp):
GTATCGATATCCCCTTCCACTATCGATACCAAATTTAGATTCGATGTTGCCTAGTATCGATACCC
TTACCATGGCATCGATACTACCATAGTATA
Found at i:1269046 original size:28 final size:28
Alignment explanation
Indices: 1268980--1269052 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 28
1268970 TTGAAGTAAC
1268980 ATAT-TTAA-AAGT-AATCAATAAAACAA
1 ATATATTAACAAGTAAAT-AATAAAACAA
* * *
1269006 ATATAGTATCAAGTAAATAATAAAACAG
1 ATATATTAACAAGTAAATAATAAAACAA
*
1269034 ATATATTAACAAGAAAATA
1 ATATATTAACAAGTAAATA
1269053 TACAACCTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
26 4 0.11
27 2 0.05
28 29 0.76
29 3 0.08
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.26
Consensus pattern (28 bp):
ATATATTAACAAGTAAATAATAAAACAA
Found at i:1270267 original size:22 final size:23
Alignment explanation
Indices: 1270211--1270273 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 23
1270201 ATTTTAAGTT
*
1270211 TTAATAG-TATATTGAATATTTTA
1 TTAATAGCTATA-TAAATATTTTA
* *
1270234 TTAAATATCTATATAAATA-TTTG
1 TT-AATAGCTATATAAATATTTTA
1270257 TTAATAGCTATATAAAT
1 TTAATAGCTATATAAAT
1270274 GTAAGTGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
22 14 0.41
23 7 0.21
24 9 0.26
25 4 0.12
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (23 bp):
TTAATAGCTATATAAATATTTTA
Found at i:1278200 original size:273 final size:265
Alignment explanation
Indices: 1277687--1278224 Score: 1004
Period size: 273 Copynumber: 2.0 Consensus size: 265
1277677 CACCAAAGAA
1277687 AAATACTGGCGCACAGGAATCTGCCAACGTGACAGAGGAGACAAGTGATGCCATGATTCTAAGCA
1 AAATACTGGCGCACAGGAATCTGCCAACGTGACAGAGGAGACAAGTGATGCCATGATTCTAAGCA
1277752 TCAACAGTCCGATTGAATCATGGATCTTGGATTCAGGGGCATCCACTCCTCATGCCGAGAAATCA
66 TCAACAGTCCGATTGAATCATGGATCTTGGATTCAGGGGCATCCACTCCTCATGCCGAGAAATCA
1277817 TGGGAACTATGTCAGTGGTGATTTTGCGAAGGTTCATCTAGCTGATGATGAAACCTTGAAGATCG
131 TGGGAACTATGTCAGTGGTGATTTTGCGAAGGTTCATCTAGCTGATGATGAAACCTTGAAGATCG
1277882 TCGGAAAAGGAGACATCCGACTAAAGCTGCCAAACCAGACCACCTGGAAGCTGACATGAGTGAGA
196 TCGGAAAAGGAGACATCCGACTAAAGCTGCCAAACCAGACCACCTGGAAGCTGACATGAGTGAGA
1277947 TATAT
261 TATAT
1277952 AAATACTGGCGCACAGGAATCTGCCAACGTGACAGAGGAGACAAGTGATGCCATGATTCTAAGCA
1 AAATACTGGCGCACAGGAATCTGCCAACGTGACAGAGGAGACAAGTGATGCCATGATTCTAAGCA
1278017 TCAACAGTCCGATTGAATCATGGATCTTGGATTCAGGGGCATCTTTCCACTCCACTCCATGCCGA
66 TCAACAGTCCGATTGAATCATGGATCTTGGATTCAGGGGCA----TCCACT-C-CT-CATGCCGA
1278082 GAAATCATGGAGAACTATGTCAGTGGTGATTTTGCGAAGGTTCATCTAGCTGATGATGAAACCTT
124 GAAATCATGG-GAACTATGTCAGTGGTGATTTTGCGAAGGTTCATCTAGCTGATGATGAAACCTT
1278147 GAAGATCGTCGGAAAAGGAGACATCCGACTAAAGCTGCCAAACCAGACCACCTGGAAGCTGACAT
188 GAAGATCGTCGGAAAAGGAGACATCCGACTAAAGCTGCCAAACCAGACCACCTGGAAGCTGACAT
1278212 GAGTGAGATATAT
253 GAGTGAGATATAT
1278225 TCATGGCCTC
Statistics
Matches: 265, Mismatches: 0, Indels: 8
0.97 0.00 0.03
Matches are distributed among these distances:
265 106 0.40
269 6 0.02
270 1 0.00
271 2 0.01
272 18 0.07
273 132 0.50
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.22
Consensus pattern (265 bp):
AAATACTGGCGCACAGGAATCTGCCAACGTGACAGAGGAGACAAGTGATGCCATGATTCTAAGCA
TCAACAGTCCGATTGAATCATGGATCTTGGATTCAGGGGCATCCACTCCTCATGCCGAGAAATCA
TGGGAACTATGTCAGTGGTGATTTTGCGAAGGTTCATCTAGCTGATGATGAAACCTTGAAGATCG
TCGGAAAAGGAGACATCCGACTAAAGCTGCCAAACCAGACCACCTGGAAGCTGACATGAGTGAGA
TATAT
Found at i:1278408 original size:15 final size:15
Alignment explanation
Indices: 1278388--1278432 Score: 90
Period size: 15 Copynumber: 3.0 Consensus size: 15
1278378 AGAGAATATC
1278388 ATTGCTGCATCAGAT
1 ATTGCTGCATCAGAT
1278403 ATTGCTGCATCAGAT
1 ATTGCTGCATCAGAT
1278418 ATTGCTGCATCAGAT
1 ATTGCTGCATCAGAT
1278433 GTTGATGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (15 bp):
ATTGCTGCATCAGAT
Found at i:1283790 original size:46 final size:46
Alignment explanation
Indices: 1283725--1283983 Score: 181
Period size: 46 Copynumber: 5.7 Consensus size: 46
1283715 TTGGAAGTGG
* * * * *
1283725 CTTTGGCGATTTCTTTGGAGGGGGAGTTCACTTGGGAGCATCCAACC
1 CTTTGGAGA-TTCATTGGAGGGCGAGCTCACTTGGGAGCATCAAACC
* * * * *
1283772 CTTTGGAGATTCATTGGAGAGCGAGCTCAGTTGAGAACGTCAAACC
1 CTTTGGAGATTCATTGGAGGGCGAGCTCACTTGGGAGCATCAAACC
* * * * * * *
1283818 CTTTAGG-TATTCATTGGAGGACAACCTCACTTGTGAACATCAAAAC
1 CTTT-GGAGATTCATTGGAGGGCGAGCTCACTTGGGAGCATCAAACC
** * * *
1283864 CTTTGGA-ATT-A-T--AGGATGAGCTCAGTTGGGAGCGTCCAACC
1 CTTTGGAGATTCATTGGAGGGCGAGCTCACTTGGGAGCATCAAACC
* *
1283905 CTTTGGAGATTCA-TGAAGGGCGAGCTCACTTGGGAGCATCGAACC
1 CTTTGGAGATTCATTGGAGGGCGAGCTCACTTGGGAGCATCAAACC
* * ** *
1283950 TTTTGAAGATTTTTTTGGGGGGCGAGCTCACTTG
1 CTTTGGAGA-TTCATTGGAGGGCGAGCTCACTTG
1283984 CTTGGAAGTA
Statistics
Matches: 165, Mismatches: 39, Indels: 16
0.75 0.18 0.07
Matches are distributed among these distances:
41 27 0.16
42 3 0.02
43 3 0.02
44 1 0.01
45 36 0.22
46 68 0.41
47 27 0.16
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (46 bp):
CTTTGGAGATTCATTGGAGGGCGAGCTCACTTGGGAGCATCAAACC
Found at i:1285351 original size:31 final size:31
Alignment explanation
Indices: 1285315--1285387 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
1285305 AGGTGAATCT
*
1285315 ATCATAAATTTGTGACGGATCCGCATATTCC
1 ATCATAAATTTGTGACGGATCCACATATTCC
* * * *
1285346 GTCATAAATTTGTGATGGGTCCACATATTCT
1 ATCATAAATTTGTGACGGATCCACATATTCC
1285377 ATCATAAATTT
1 ATCATAAATTT
1285388 AAAATATTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (31 bp):
ATCATAAATTTGTGACGGATCCACATATTCC
Found at i:1286997 original size:31 final size:29
Alignment explanation
Indices: 1286942--1287004 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
1286932 TAAAATTACA
1286942 ATATCAAACAAAAAAAAAAAGATAAATGC
1 ATATCAAACAAAAAAAAAAAGATAAATGC
*
1286971 ATAT-AAATAAAAAAAATTAAAGGATAAATGC
1 ATATCAAACAAAAAAAA--AAA-GATAAATGC
1287002 ATA
1 ATA
1287005 AATCGATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 11 0.37
29 4 0.13
30 3 0.10
31 12 0.40
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.19
Consensus pattern (29 bp):
ATATCAAACAAAAAAAAAAAGATAAATGC
Found at i:1288394 original size:39 final size:38
Alignment explanation
Indices: 1288340--1288469 Score: 143
Period size: 39 Copynumber: 3.3 Consensus size: 38
1288330 ATGAACCAGA
* * * * *
1288340 GGTAAAGACTTACCCTGTGAACAAAGCAGAAGAGCATGC
1 GGTAAGGACTTACCCTGAGCACAAAGC-GAGGAGCCTGC
*
1288379 GGTAAGGACTTACCCTGAGCACAAAGTCGAGGAGCCTGT
1 GGTAAGGACTTACCCTGAGCACAAAG-CGAGGAGCCTGC
* * * *
1288418 GGAAAGGACTTACCCTGGGCACAAATCTGGGGAGCCTGC
1 GGTAAGGACTTACCCTGAGCACAAAGC-GAGGAGCCTGC
1288457 GGTAAGGACTTAC
1 GGTAAGGACTTAC
1288470 AAGTCATAGA
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
38 1 0.01
39 75 0.97
40 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.30, T:0.17
Consensus pattern (38 bp):
GGTAAGGACTTACCCTGAGCACAAAGCGAGGAGCCTGC
Found at i:1291486 original size:24 final size:22
Alignment explanation
Indices: 1291435--1291479 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 22
1291425 AAGGTCGTGT
*
1291435 CACTTGCCTTCGACCATGGCCA
1 CACTTGCCTACGACCATGGCCA
1291457 CGACTTGGCCTACGACCAATGGC
1 C-ACTT-GCCTACGACC-ATGGC
1291480 AGCACTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 1 0.05
23 4 0.21
24 9 0.47
25 5 0.26
ACGTcount: A:0.20, C:0.38, G:0.22, T:0.20
Consensus pattern (22 bp):
CACTTGCCTACGACCATGGCCA
Found at i:1292324 original size:39 final size:38
Alignment explanation
Indices: 1292259--1292431 Score: 202
Period size: 39 Copynumber: 4.4 Consensus size: 38
1292249 GTATAAGGAT
* * **
1292259 CTGCGATAAGGACATACCCTATGCACAAAGCAGAGGAGC
1 CTGCGGTAAGGACTTACCCTGGGCACAAAGC-GAGGAGC
*
1292298 ATGCGGTAAGGACTTACCCTGGGCACAAAGTCGAGGAGC
1 CTGCGGTAAGGACTTACCCTGGGCACAAAG-CGAGGAGC
* * ** *
1292337 CTGCGGTAAGGAGTTTCCCTGAACACAAAATCGAGGAGC
1 CTGCGGTAAGGACTTACCCTGGGCAC-AAAGCGAGGAGC
*
1292376 CTGCGGTAAGGACTTACCCTGGGAACAAAGCCGAGGAGC
1 CTGCGGTAAGGACTTACCCTGGGCACAAAG-CGAGGAGC
*
1292415 CTGCAGTAAGGACTTAC
1 CTGCGGTAAGGACTTAC
1292432 AAGTCATAGA
Statistics
Matches: 113, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
38 3 0.03
39 106 0.94
40 4 0.04
ACGTcount: A:0.31, C:0.24, G:0.29, T:0.16
Consensus pattern (38 bp):
CTGCGGTAAGGACTTACCCTGGGCACAAAGCGAGGAGC
Found at i:1293363 original size:2 final size:2
Alignment explanation
Indices: 1293350--1293395 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
1293340 GTGAGGCATA
*
1293350 AT AT AA AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1293391 AT AT A
1 AT AT A
1293396 AACAATGCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1293688 original size:20 final size:18
Alignment explanation
Indices: 1293647--1293713 Score: 89
Period size: 18 Copynumber: 3.6 Consensus size: 18
1293637 TATTTGTCCT
1293647 GAAGGACCACTATGTCTC
1 GAAGGACCACTATGTCTC
*
1293665 GAAGGACCACTGATTGTTTC
1 GAAGGACCACT-A-TGTCTC
* *
1293685 GAAGAACCACTATGTCCC
1 GAAGGACCACTATGTCTC
1293703 GAAGGACCACT
1 GAAGGACCACT
1293714 GATAATGCCT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 25 0.60
19 2 0.05
20 15 0.36
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.21
Consensus pattern (18 bp):
GAAGGACCACTATGTCTC
Found at i:1294359 original size:64 final size:63
Alignment explanation
Indices: 1294285--1294424 Score: 169
Period size: 64 Copynumber: 2.2 Consensus size: 63
1294275 ATCCCTTGAC
1294285 GGGTGCATCGATGCACAA-TCTATGCATCGATACA-TAA-ATCTATTTCGATGTTTGTATTTTAA
1 GGGTGCATCGATGCACAACT-TATGCATCGATACACTAATA-C-ATTT-GATGTTTGTATTTTAA
*
1294347 GG
62 AG
* * *
1294349 GGGTGCATCGATGCACTACTTGTGCATCGATACACTAATGACATTTGATGTTTTTATTTTAAAG
1 GGGTGCATCGATGCACAACTTATGCATCGATACACTAAT-ACATTTGATGTTTGTATTTTAAAG
*
1294413 GAGTGCATCGAT
1 GGGTGCATCGAT
1294425 ACACCTAGAA
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
64 57 0.85
65 8 0.12
66 1 0.01
67 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (63 bp):
GGGTGCATCGATGCACAACTTATGCATCGATACACTAATACATTTGATGTTTGTATTTTAAAG
Found at i:1295426 original size:7 final size:7
Alignment explanation
Indices: 1295410--1295474 Score: 55
Period size: 7 Copynumber: 9.7 Consensus size: 7
1295400 CAACGATCGA
*
1295410 TCAACAG
1 TCAACGG
1295417 TCAACGG
1 TCAACGG
*
1295424 TCACCGG
1 TCAACGG
1295431 T---CGG
1 TCAACGG
1295435 TCAACGG
1 TCAACGG
*
1295442 TCAATGG
1 TCAACGG
*
1295449 TTAACGG
1 TCAACGG
* *
1295456 TCAGCGA
1 TCAACGG
1295463 TCAACGG
1 TCAACGG
1295470 TCAAC
1 TCAAC
1295475 AACTGACCAG
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
4 4 0.09
7 41 0.91
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (7 bp):
TCAACGG
Found at i:1295456 original size:25 final size:25
Alignment explanation
Indices: 1295396--1295474 Score: 77
Period size: 25 Copynumber: 3.0 Consensus size: 25
1295386 AAGTCAATGT
* * *
1295396 CGGTCAACGATCGATCAACAGTCAA
1 CGGTCAACGGTCGGTCAACGGTCAA
*
1295421 CGGTCACCGGTCGGTCAACGGTCAA
1 CGGTCAACGGTCGGTCAACGGTCAA
* *
1295446 TGGTTAACGGTCAGCGATCAACGGTCAA
1 CGGTCAACGGTC-G-G-TCAACGGTCAA
1295474 C
1 C
1295475 AACTGACCAG
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
25 30 0.70
26 1 0.02
27 1 0.02
28 11 0.26
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.18
Consensus pattern (25 bp):
CGGTCAACGGTCGGTCAACGGTCAA
Found at i:1298931 original size:34 final size:34
Alignment explanation
Indices: 1298871--1298937 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
1298861 CCAAATAGGA
*
1298871 TAAAAATTTATTAGGATAGAAAATAAACATATTT
1 TAAAAATTTATTAGAATAGAAAATAAACATATTT
*
1298905 TAAAAATTTTATTA-AATA-AAATATAAATATATT
1 TAAAAA-TTTATTAGAATAGAAA-ATAAACATATT
1298938 GACTATATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 3 0.10
34 19 0.66
35 7 0.24
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.39
Consensus pattern (34 bp):
TAAAAATTTATTAGAATAGAAAATAAACATATTT
Found at i:1301680 original size:10 final size:10
Alignment explanation
Indices: 1301665--1301700 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
1301655 TAACCAAAAC
1301665 ATATCATAAA
1 ATATCATAAA
1301675 ATATCA-AAA
1 ATATCATAAA
1301684 TATATCATAAA
1 -ATATCATAAA
1301695 ATATCA
1 ATATCA
1301701 AAATATGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 3 0.12
10 18 0.75
11 3 0.12
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (10 bp):
ATATCATAAA
Found at i:1301688 original size:20 final size:20
Alignment explanation
Indices: 1301659--1301706 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1301649 GAGGTGTAAC
*
1301659 CAAAACATATCATAAAATAT
1 CAAAATATATCATAAAATAT
1301679 CAAAATATATCATAAAATAT
1 CAAAATATATCATAAAATAT
1301699 CAAAATAT
1 CAAAATAT
1301707 GAATTTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.27
Consensus pattern (20 bp):
CAAAATATATCATAAAATAT
Found at i:1301706 original size:8 final size:9
Alignment explanation
Indices: 1301659--1301703 Score: 54
Period size: 10 Copynumber: 4.6 Consensus size: 9
1301649 GAGGTGTAAC
1301659 CAAAACATAT
1 CAAAA-ATAT
1301669 CATAAAATAT
1 CA-AAAATAT
1301679 CAAAATATAT
1 CAAAA-ATAT
1301689 CATAAAATAT
1 CA-AAAATAT
1301699 CAAAA
1 CAAAA
1301704 TATGAATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
9 6 0.19
10 20 0.62
11 6 0.19
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.24
Consensus pattern (9 bp):
CAAAAATAT
Found at i:1308026 original size:22 final size:21
Alignment explanation
Indices: 1308001--1308044 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
1307991 AACCGACCGA
*
1308001 ACCGAATTAGTTCGGTTCGGTT
1 ACCGAATTAGTTAGG-TCGGTT
1308023 ACCGAATTAGTTAGGTCGGTT
1 ACCGAATTAGTTAGGTCGGTT
1308044 A
1 A
1308045 ACGGTTAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (21 bp):
ACCGAATTAGTTAGGTCGGTT
Found at i:1309107 original size:185 final size:186
Alignment explanation
Indices: 1308789--1309161 Score: 635
Period size: 185 Copynumber: 2.0 Consensus size: 186
1308779 ATTAAATTTT
1308789 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
* *
1308854 TTTAAGATTCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
66 TTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
**
1308919 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTATTTTTT-AATTAAAA
131 TTATTTTATAATTATATATTATTTAAATTAATAATAAACTATTTTTTGAATTAAAA
* *
1308974 AAATATTATATATATTATATATAACATATGGGCT-AAGCCCAAACTATTTAAAACCCAATTAATA
1 AAATATTAAATATATTATATATAACATATGGGCTCAA-CCCAAACCATTTAAAACCCAATTAATA
*
1309038 ATTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAAATTATCTGAAA-T
65 ATTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAAATTATAT-AAATT
*
1309102 TTTTATTTTATAATTATATATTATTTAAATTAATAATAAACTTTTTTTTGAATTAAAA
129 TTTTATTTTATAATTATATATTATTTAAATTAATAATAAACTATTTTTTGAATTAAAA
1309160 AA
1 AA
1309162 CATTTATTTT
Statistics
Matches: 177, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
184 2 0.01
185 162 0.92
186 13 0.07
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (186 bp):
AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAAATTATATAAATTTT
TTATTTTATAATTATATATTATTTAAATTAATAATAAACTATTTTTTGAATTAAAA
Found at i:1313558 original size:35 final size:35
Alignment explanation
Indices: 1313512--1313582 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
1313502 CATTTGATAT
1313512 TAATTAAAACATTCTTTTAGGGTTAATTAAGTTCA
1 TAATTAAAACATTCTTTTAGGGTTAATTAAGTTCA
* *
1313547 TAATTCAAACATTCTTTTATGGTTAATTAAGTTCA
1 TAATTAAAACATTCTTTTAGGGTTAATTAAGTTCA
1313582 T
1 T
1313583 TTTTCTTTCG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (35 bp):
TAATTAAAACATTCTTTTAGGGTTAATTAAGTTCA
Found at i:1316855 original size:27 final size:27
Alignment explanation
Indices: 1316825--1316883 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
1316815 TTTGCTTCAA
* *
1316825 CATCTGCAACTGAAAATTACTATAATG
1 CATCTACAACTGAAAACTACTATAATG
* *
1316852 CATCTACAGCTGAAGACTACTATAATG
1 CATCTACAACTGAAAACTACTATAATG
1316879 CATCT
1 CATCT
1316884 CAGACTAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (27 bp):
CATCTACAACTGAAAACTACTATAATG
Found at i:1330772 original size:2 final size:2
Alignment explanation
Indices: 1330759--1330813 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
1330749 CTATTTAATC
*
1330759 TA TA TA TC 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
1330801 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
1330814 CATTACGCTA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1334297 original size:22 final size:22
Alignment explanation
Indices: 1334272--1334316 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1334262 CCGATTATTT
*
1334272 TATATATGATTTTTATCATGAA
1 TATATATGATGTTTATCATGAA
*
1334294 TATATATGATGTTTATTATGAA
1 TATATATGATGTTTATCATGAA
1334316 T
1 T
1334317 GTTACTTTGG
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:0.36, C:0.02, G:0.11, T:0.51
Consensus pattern (22 bp):
TATATATGATGTTTATCATGAA
Found at i:1334623 original size:61 final size:61
Alignment explanation
Indices: 1334493--1334610 Score: 182
Period size: 61 Copynumber: 1.9 Consensus size: 61
1334483 AAGGACACTA
* * **
1334493 AGTGCAGGTGGAGGGCACAACCTTATGTGTCATATCCAGATTAGCACTAGAGTGTAAACCT
1 AGTGTAGGTGGAGGGCACAACCTTATGTCTCATATCCAGATTAGCACTAGAGCATAAACCT
* *
1334554 AGTGTAGGTGGTGGGCACAACCTTATGTCTCTTATCCAGATTAGCACTAGAGCATAA
1 AGTGTAGGTGGAGGGCACAACCTTATGTCTCATATCCAGATTAGCACTAGAGCATAA
1334611 GTTTAGTTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.26
Consensus pattern (61 bp):
AGTGTAGGTGGAGGGCACAACCTTATGTCTCATATCCAGATTAGCACTAGAGCATAAACCT
Found at i:1334957 original size:3 final size:3
Alignment explanation
Indices: 1334909--1334942 Score: 50
Period size: 3 Copynumber: 10.7 Consensus size: 3
1334899 GTAAAAATAT
1334909 TTA TTA TTA TTAA GTTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TT-A -TTA TTA TTA TTA TTA TTA TT
1334943 TACATTTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 25 0.86
4 2 0.07
5 2 0.07
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1336234 original size:29 final size:30
Alignment explanation
Indices: 1336196--1336379 Score: 192
Period size: 30 Copynumber: 6.2 Consensus size: 30
1336186 GGTTTTTTTA
*
1336196 TTTATTCCCTTAAGTTTATGTTTTTGCTAT
1 TTTAGTCCCTTAAGTTTATGTTTTTGCTAT
* * *
1336226 TTTA-ACCCTTAAGTTTTTGTTCTTGCTAT
1 TTTAGTCCCTTAAGTTTATGTTTTTGCTAT
*
1336255 TTTAG-CCCTTTAAGTTTATGTTTTTGTTAT
1 TTTAGTCCC-TTAAGTTTATGTTTTTGCTAT
* * * *
1336285 TTTAGTCCATTAAATTTATATTTTTTCTAT
1 TTTAGTCCCTTAAGTTTATGTTTTTGCTAT
* * ** *
1336315 TTTAGTCCTTTAAATTTAAATTTTTGTTAT
1 TTTAGTCCCTTAAGTTTATGTTTTTGCTAT
* * *
1336345 TTTAGTCCCTTAAGTTTCTCTTTTTTCTAT
1 TTTAGTCCCTTAAGTTTATGTTTTTGCTAT
1336375 TTTAG
1 TTTAG
1336380 CACTTTAAAT
Statistics
Matches: 129, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
29 29 0.22
30 98 0.76
31 2 0.02
ACGTcount: A:0.20, C:0.12, G:0.09, T:0.59
Consensus pattern (30 bp):
TTTAGTCCCTTAAGTTTATGTTTTTGCTAT
Found at i:1336339 original size:60 final size:59
Alignment explanation
Indices: 1336205--1336418 Score: 216
Period size: 60 Copynumber: 3.6 Consensus size: 59
1336195 ATTTATTCCC
* * * * * * * * *
1336205 TTAAGTTTATGTTTTTGCTATTTTA-ACCCTTAAGTTTTTGTTCTTGCTATTTTAGCCCT
1 TTAAATTTATATTTTTGTTATTTTAGTCCCTTAAATTTATATTTTTTCTATTTTAG-CCT
* * *
1336264 TTAAGTTTATGTTTTTGTTATTTTAGTCCATTAAATTTATATTTTTTCTATTTTAGTCCT
1 TTAAATTTATATTTTTGTTATTTTAGTCCCTTAAATTTATATTTTTTCTATTTTAG-CCT
* * * *
1336324 TTAAATTTAAATTTTTGTTATTTTAGTCCCTTAAGTTTCTCTTTTTTCTATTTTAGCACT
1 TTAAATTTATATTTTTGTTATTTTAGTCCCTTAAATTTATATTTTTTCTATTTTAGC-CT
* *
1336384 TTAAATTTATA-TTATGTTTATTTTGGTCCCTTAAA
1 TTAAATTTATATTTTTG-TTATTTTAGTCCCTTAAA
1336419 ATCCTTAAAT
Statistics
Matches: 132, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
59 29 0.22
60 103 0.78
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.58
Consensus pattern (59 bp):
TTAAATTTATATTTTTGTTATTTTAGTCCCTTAAATTTATATTTTTTCTATTTTAGCCT
Found at i:1336358 original size:90 final size:90
Alignment explanation
Indices: 1336252--1336418 Score: 216
Period size: 90 Copynumber: 1.9 Consensus size: 90
1336242 TTGTTCTTGC
* *
1336252 TATTTTAGCCCTTTAAGTTTATGTTTTTGT-TATTTTAGTC-CATTAAATTTATATT-TTTTCTA
1 TATTTTAGCCCTTTAAGTTTATCTTTTT-TCTATTTTAG-CACATTAAATTTATATTATGTT-TA
*
1336314 TTTTAGTCCTTTAAATTTAAATTTTTGT
63 TTTTAGTCCCTTAAATTTAAATTTTTGT
* *
1336342 TATTTTAGTCCC-TTAAGTTTCTCTTTTTTCTATTTTAGCACTTTAAATTTATATTATGTTTATT
1 TATTTTAG-CCCTTTAAGTTTATCTTTTTTCTATTTTAGCACATTAAATTTATATTATGTTTATT
*
1336406 TTGGTCCCTTAAA
65 TTAGTCCCTTAAA
1336419 ATCCTTAAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
89 2 0.03
90 59 0.88
91 6 0.09
ACGTcount: A:0.23, C:0.11, G:0.08, T:0.58
Consensus pattern (90 bp):
TATTTTAGCCCTTTAAGTTTATCTTTTTTCTATTTTAGCACATTAAATTTATATTATGTTTATTT
TAGTCCCTTAAATTTAAATTTTTGT
Found at i:1336406 original size:30 final size:29
Alignment explanation
Indices: 1336252--1336418 Score: 165
Period size: 30 Copynumber: 5.6 Consensus size: 29
1336242 TTGTTCTTGC
* * *
1336252 TATTTTAGCCCTTTAAGTTTATGTTTTTGT
1 TATTTTAGTCCTTTAAATTTATATTTTT-T
*
1336282 TATTTTAGTCCATTAAATTTATATTTTTT
1 TATTTTAGTCCTTTAAATTTATATTTTTT
*
1336311 CTATTTTAGTCCTTTAAATTTAAATTTTTGT
1 -TATTTTAGTCCTTTAAATTTATATTTTT-T
* * * *
1336342 TATTTTAGTCCCTTAAGTTTCTCTTTTTT
1 TATTTTAGTCCTTTAAATTTATATTTTTT
*
1336371 CTATTTTAG-CACTTTAAATTTATATTATGTT
1 -TATTTTAGTC-CTTTAAATTTATATT-TTTT
* *
1336402 TATTTTGGTCCCTTAAA
1 TATTTTAGTCCTTTAAA
1336419 ATCCTTAAAT
Statistics
Matches: 113, Mismatches: 18, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
29 3 0.03
30 105 0.93
31 5 0.04
ACGTcount: A:0.23, C:0.11, G:0.08, T:0.58
Consensus pattern (29 bp):
TATTTTAGTCCTTTAAATTTATATTTTTT
Found at i:1343468 original size:61 final size:61
Alignment explanation
Indices: 1343343--1343460 Score: 164
Period size: 61 Copynumber: 1.9 Consensus size: 61
1343333 AGGGACACTA
* * *
1343343 AGTGTAGGTGGAGGGCACAACCTTACGTGTCCTATCCGGATTAGCACTAGAGTGTAAACCT
1 AGTGTAGGTGGAGGGCACAACCTTACGTGTCATATCCAGACTAGCACTAGAGTGTAAACCT
* * * * *
1343404 AGTGTAGGTGGTGGGCACGACCTTATGTGTCATATCTAGACTAGTACTAGAGTGTAA
1 AGTGTAGGTGGAGGGCACAACCTTACGTGTCATATCCAGACTAGCACTAGAGTGTAA
1343461 GCTTAGTGCA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (61 bp):
AGTGTAGGTGGAGGGCACAACCTTACGTGTCATATCCAGACTAGCACTAGAGTGTAAACCT
Found at i:1344492 original size:44 final size:44
Alignment explanation
Indices: 1344424--1344526 Score: 116
Period size: 44 Copynumber: 2.3 Consensus size: 44
1344414 ATCAATACCC
* *
1344424 GTATCAGTACAACTGTGTAATTTTACACACTAGTAGCGATACAT
1 GTATCGGTACAACTATGTAATTTTACACACTAGTAGCGATACAT
* * * * * * *
1344468 GTATCGGTACTACTATGTATTTTTACACATTGGTATCTATACCT
1 GTATCGGTACAACTATGTAATTTTACACACTAGTAGCGATACAT
*
1344512 GTATCGGTACCACTA
1 GTATCGGTACAACTA
1344527 GAAAAATATC
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (44 bp):
GTATCGGTACAACTATGTAATTTTACACACTAGTAGCGATACAT
Found at i:1348086 original size:19 final size:18
Alignment explanation
Indices: 1348044--1348088 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
1348034 CTAAATCATT
*
1348044 TTTCAAAATCATTTTGAT
1 TTTCAAAATCATTTTGAC
1348062 TTTCAAAATCAACTTTTG-C
1 TTTCAAAATC-A-TTTTGAC
1348081 TTTCAAAA
1 TTTCAAAA
1348089 CTAAATCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 10 0.42
19 9 0.38
20 5 0.21
ACGTcount: A:0.36, C:0.16, G:0.04, T:0.44
Consensus pattern (18 bp):
TTTCAAAATCATTTTGAC
Found at i:1348945 original size:23 final size:23
Alignment explanation
Indices: 1348919--1348967 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
1348909 TCGGTTCTTT
1348919 CATGAGTGACTTAGAGCTTATCC
1 CATGAGTGACTTAGAGCTTATCC
1348942 CATGAGTGACTTAGAGCTTATCC
1 CATGAGTGACTTAGAGCTTATCC
1348965 CAT
1 CAT
1348968 ATCTCATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (23 bp):
CATGAGTGACTTAGAGCTTATCC
Found at i:1351492 original size:105 final size:105
Alignment explanation
Indices: 1351292--1351512 Score: 317
Period size: 105 Copynumber: 2.1 Consensus size: 105
1351282 GTGTTTGAAA
*
1351292 TGAATTAATTGCTTTATGAAAAAACTAACATTTTCTGAAATGAATTTATTTATCACTAAAAATTT
1 TGAATTAATTGCTTTATGAAAAAACTAACATTTTCTAAAATGAATTTATTTATCACTAAAAATTT
1351357 TCTGAAATGAAGTGATATATCAATGAAAAAGTGTCTA-AAG
66 TCTGAAATGAAGTGATATATCAATGAAAAAGTGTC-AGAAG
* * * *
1351397 TGAATTAATTG-TTGTA-GGAAAAA-TGACATTTTTCTAAAATGATTTTATTTATCACTAAAACG
1 TGAATTAATTGCTT-TATGAAAAAACTAACA-TTTTCTAAAATGAATTTATTTATCACTAAAA-A
1351459 TTTTCTGAAAATGAAGTGATATATCAATG-AAAAGTGTCAGAAG
63 TTTTCTG-AAATGAAGTGATATATCAATGAAAAAGTGTCAGAAG
1351502 TGAATTAATTG
1 TGAATTAATTG
1351513 GCCACTTAAA
Statistics
Matches: 106, Mismatches: 5, Indels: 10
0.88 0.04 0.08
Matches are distributed among these distances:
103 4 0.04
104 38 0.36
105 43 0.41
106 21 0.20
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (105 bp):
TGAATTAATTGCTTTATGAAAAAACTAACATTTTCTAAAATGAATTTATTTATCACTAAAAATTT
TCTGAAATGAAGTGATATATCAATGAAAAAGTGTCAGAAG
Found at i:1352893 original size:44 final size:44
Alignment explanation
Indices: 1352812--1352927 Score: 124
Period size: 44 Copynumber: 2.6 Consensus size: 44
1352802 ACTTAAAGGG
* * *
1352812 AGTATCGAAACCCGTATCGATACTACTGTGTAATTTTACACACT
1 AGTATCGATACCTGTATCGATACTACTATGTAATTTTACACACT
* * * * * *
1352856 AGTATCGGTACCTGTATCGGTACTGCTATGTATTTTTATACATT
1 AGTATCGATACCTGTATCGATACTACTATGTAATTTTACACACT
* * *
1352900 GGTATCGATACCTATATCGATACCACTA
1 AGTATCGATACCTGTATCGATACTACTA
1352928 GAACAGTATT
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
44 57 1.00
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (44 bp):
AGTATCGATACCTGTATCGATACTACTATGTAATTTTACACACT
Done.