Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007721.1 Hibiscus syriacus cultivar Beakdansim tig00109957_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: 3738426
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 16
Found at i:1276121 original size:8 final size:7
Alignment explanation
Indices: 1276102--1276155 Score: 54
Period size: 8 Copynumber: 7.0 Consensus size: 7
1276092 TAATTAAAAT
1276102 TATTTTA
1 TATTTTA
1276109 TATTTTAA
1 TATTTT-A
1276117 TATTTAGTA
1 TATTT--TA
*
1276126 TATTTTT
1 TATTTTA
1276133 TATTTTA
1 TATTTTA
1276140 TAATTTTA
1 T-ATTTTA
1276148 TGATTTTA
1 T-ATTTTA
1276156 AAATATTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
7 14 0.35
8 19 0.47
9 6 0.15
10 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (7 bp):
TATTTTA
Found at i:1278377 original size:20 final size:19
Alignment explanation
Indices: 1278352--1278403 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 19
1278342 TGATTCAATC
1278352 AGTATCGATACCGAAGAGA
1 AGTATCGATACCGAAGAGA
*
1278371 GAGTATCGATACCGAAGTGA
1 -AGTATCGATACCGAAGAGA
1278391 AGGTATCGATACC
1 A-GTATCGATACC
1278404 ATTTTGAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.37, C:0.17, G:0.27, T:0.19
Consensus pattern (19 bp):
AGTATCGATACCGAAGAGA
Found at i:1278468 original size:19 final size:19
Alignment explanation
Indices: 1278425--1278468 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1278415 GAATGCAAAA
* *
1278425 ATGGTATCGATACCATGGG
1 ATGGTATCAATACCATAGG
* *
1278444 AAGGTATCAATACCATAGT
1 ATGGTATCAATACCATAGG
1278463 ATGGTA
1 ATGGTA
1278469 GTATCGATAC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (19 bp):
ATGGTATCAATACCATAGG
Found at i:1278478 original size:22 final size:20
Alignment explanation
Indices: 1278428--1278498 Score: 63
Period size: 22 Copynumber: 3.5 Consensus size: 20
1278418 TGCAAAAATG
* * *
1278428 GTATCGATACCATGGGAAG-
1 GTATCGATACCATAGTAGGA
*
1278447 GTATCAATACCATAGTATGGTA
1 GTATCGATACCATAGTA-GG-A
* *
1278469 GTATCGATACCATGGTAGGG
1 GTATCGATACCATAGTAGGA
1278489 GTATCGATAC
1 GTATCGATAC
1278499 TGAGGAACCA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
19 14 0.33
20 11 0.26
21 2 0.05
22 15 0.36
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (20 bp):
GTATCGATACCATAGTAGGA
Found at i:1278965 original size:45 final size:42
Alignment explanation
Indices: 1278914--1279295 Score: 243
Period size: 45 Copynumber: 9.5 Consensus size: 42
1278904 ATAAAAGAAT
*
1278914 AATGCATATGGGTGCATTATTGGCATGAAATGATGTCTTAGATGA
1 AATGCATATGGGTGCATTATCGGCATGAAATGATG-CTTA-AT-A
*
1278959 AATGCATATGGGTGCATTATCGACAT-AAA--A-G---AAT-
1 AATGCATATGGGTGCATTATCGGCATGAAATGATGCTTAATA
* *
1278993 AATGCATATGGGTGCATTATTGGCATGAAATGATGCCTTATCTGA
1 AATGCATATGGGTGCATTATCGGCATGAAATGATG-CTTA-AT-A
* *
1279038 AATGCATATGTGTGCATTATCGACAT-AAA--A-G---AAT-
1 AATGCATATGGGTGCATTATCGGCATGAAATGATGCTTAATA
* *
1279072 AATGCATATGGGTGCATTATTGGCATGAAATGATGCCTTAGCTGA
1 AATGCATATGGGTGCATTATCGGCATGAAATGATG-CTTA-AT-A
*
1279117 AATGCATATGGGTGCATTATCGGTAT-AAA--A-G---AAT-
1 AATGCATATGGGTGCATTATCGGCATGAAATGATGCTTAATA
* *
1279151 AATGCATATGGGTGCATTATTGGCATGAAATGATGCCTTAGCTTA
1 AATGCATATGGGTGCATTATCGGCATGAAATGATG-CTTA--ATA
1279196 AATGCATATGGGTGCATTATCGGCAT-AAA--A-G---AAT-
1 AATGCATATGGGTGCATTATCGGCATGAAATGATGCTTAATA
** * * * **
1279230 AATGCATATGTATGCATTATTGGCATGAGAGGATGCCAAAGTTGA
1 AATGCATATGGGTGCATTATCGGCATGAAATGATGCTTAA--T-A
1279275 AATGCATATGGGTGCATTATC
1 AATGCATATGGGTGCATTATC
1279296 AACATAAAAG
Statistics
Matches: 265, Mismatches: 28, Indels: 88
0.70 0.07 0.23
Matches are distributed among these distances:
34 94 0.35
35 12 0.05
36 4 0.02
37 8 0.03
38 4 0.02
41 6 0.02
42 7 0.03
43 3 0.01
44 13 0.05
45 114 0.43
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.31
Consensus pattern (42 bp):
AATGCATATGGGTGCATTATCGGCATGAAATGATGCTTAATA
Found at i:1278990 original size:79 final size:79
Alignment explanation
Indices: 1278904--1279305 Score: 660
Period size: 79 Copynumber: 5.1 Consensus size: 79
1278894 GAACGAATGA
* *
1278904 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAATGATGTCTTAGATGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAATGATGCCTTAGCTGAAATGCATATG
1278969 GGTGCATTATCGAC
66 GGTGCATTATCGAC
*
1278983 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAATGATGCCTTATCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAATGATGCCTTAGCTGAAATGCATATG
*
1279048 TGTGCATTATCGAC
66 GGTGCATTATCGAC
1279062 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAATGATGCCTTAGCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAATGATGCCTTAGCTGAAATGCATATG
**
1279127 GGTGCATTATCGGT
66 GGTGCATTATCGAC
*
1279141 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAATGATGCCTTAGCTTAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAATGATGCCTTAGCTGAAATGCATATG
*
1279206 GGTGCATTATCGGC
66 GGTGCATTATCGAC
** * * ** *
1279220 ATAAAAGAATAATGCATATGTATGCATTATTGGCATGAGAGGATGCCAAAGTTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAATGATGCCTTAGCTGAAATGCATATG
*
1279285 GGTGCATTATCAAC
66 GGTGCATTATCGAC
1279299 ATAAAAG
1 ATAAAAG
1279306 TATGCTATAA
Statistics
Matches: 303, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 303 1.00
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.30
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAATGATGCCTTAGCTGAAATGCATATG
GGTGCATTATCGAC
Found at i:1278997 original size:34 final size:34
Alignment explanation
Indices: 1278959--1279255 Score: 180
Period size: 34 Copynumber: 7.8 Consensus size: 34
1278949 TCTTAGATGA
*
1278959 AATGCATATGGGTGCATTATCGACATAAAAGAAT
1 AATGCATATGGGTGCATTATCGGCATAAAAGAAT
* *
1278993 AATGCATATGGGTGCATTATTGGCATGAAATGATGCCTTATCT
1 AATGCATATGGGTGCATTATCGGCAT-AAA--A-G----A-AT
* *
1279036 GAAATGCATATGTGTGCATTATCGACATAAAAGAAT
1 --AATGCATATGGGTGCATTATCGGCATAAAAGAAT
* *
1279072 AATGCATATGGGTGCATTATTGGCATGAAATGATGCCTTAGCT
1 AATGCATATGGGTGCATTATCGGCAT-AAA--A-G----A-AT
*
1279115 GAAATGCATATGGGTGCATTATCGGTATAAAAGAAT
1 --AATGCATATGGGTGCATTATCGGCATAAAAGAAT
* *
1279151 AATGCATATGGGTGCATTATTGGCATGAAATGATGCCTTAGCTT
1 AATGCATATGGGTGCATTATCGGCAT-AAA--A-G----A--AT
1279195 AAATGCATATGGGTGCATTATCGGCATAAAAGAAT
1 -AATGCATATGGGTGCATTATCGGCATAAAAGAAT
** *
1279230 AATGCATATGTATGCATTATTGGCAT
1 AATGCATATGGGTGCATTATCGGCAT
1279256 GAGAGGATGC
Statistics
Matches: 208, Mismatches: 22, Indels: 66
0.70 0.07 0.22
Matches are distributed among these distances:
34 94 0.45
35 10 0.05
36 2 0.01
37 6 0.03
38 3 0.01
41 3 0.01
42 6 0.03
43 2 0.01
44 10 0.05
45 72 0.35
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATCGGCATAAAAGAAT
Found at i:1281031 original size:22 final size:22
Alignment explanation
Indices: 1281001--1281043 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1280991 TGTTCAATTT
1281001 TATTATTAA-TATTCTAGAATAA
1 TATTATTAATTATTCTA-AATAA
*
1281023 TATTGTTAATTATTCTAAATA
1 TATTATTAATTATTCTAAATA
1281044 TCCTAATCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.49
Consensus pattern (22 bp):
TATTATTAATTATTCTAAATAA
Found at i:1284593 original size:30 final size:30
Alignment explanation
Indices: 1284534--1284610 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
1284524 TTTATTTTTA
*
1284534 TTTAAAAATATATTTTATTCCTATCTTAAC
1 TTTAAAAATATATTTTATTCCTATATTAAC
* *
1284564 TTTAAAAATATATTTTACTT-TTTTATTAAC
1 TTTAAAAATATATTTTA-TTCCTATATTAAC
* *
1284594 -TTAACAATATTTTTTAT
1 TTTAAAAATATATTTTAT
1284611 ATCTTAACTT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 1 0.02
29 14 0.34
30 24 0.59
31 2 0.05
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (30 bp):
TTTAAAAATATATTTTATTCCTATATTAAC
Found at i:1285386 original size:81 final size:81
Alignment explanation
Indices: 1285296--1285866 Score: 903
Period size: 81 Copynumber: 7.1 Consensus size: 81
1285286 TTATAAAATA
* * *
1285296 AAAAGATTAATGGTCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATACCAGTAAGATGAAAGG
1 AAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGG
1285361 TTAAATACCTTTGAGT
66 TTAAATACCTTTGAGT
*
1285377 AAAAGATTAATGGCCTAGCTGTGCATTTGACAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGG
1 AAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGG
1285442 TTAAATACCTTTGAGT
66 TTAAATACCTTTGAGT
* *
1285458 AAAAGATTAATAGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGG
1 AAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGG
*
1285523 TTAAATACC--TGAGC
66 TTAAATACCTTTGAGT
* * *
1285537 AAAAGATTAATGGCCTAGTTATGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGG
1 AAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGG
1285602 TTAAATACCTTTGAGT
66 TTAAATACCTTTGAGT
* *
1285618 AAAAGATTAATGGCCTAGATGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGT
1 AAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGG
1285683 TTAAATACCTTTGAGT
66 TTAAATACCTTTGAGT
* * *
1285699 AAAAGATTAATGGTCAAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGG
1 AAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGG
1285764 TTAAATACCTTTGAGT
66 TTAAATACCTTTGAGT
* * * ** * * * *
1285780 ACAAGATTAATGGCCTAGCTATGTATTTGGGAGGAATGTGTCAATCATGCAAGTTAGATGAAAGG
1 AAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGG
*
1285845 TTAAATACCTTTGGGT
66 TTAAATACCTTTGAGT
1285861 AAAAGA
1 AAAAGA
1285867 CAAAATGCTT
Statistics
Matches: 455, Mismatches: 33, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
79 75 0.16
81 380 0.84
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (81 bp):
AAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGG
TTAAATACCTTTGAGT
Found at i:1285724 original size:241 final size:242
Alignment explanation
Indices: 1285296--1285866 Score: 910
Period size: 241 Copynumber: 2.4 Consensus size: 242
1285286 TTATAAAATA
* * * * *
1285296 AAAAGATTAATGGTCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATACCAGTAAGATGAAAGG
1 AAAAGATTAATGGCCTAGCTATGCATTTGACAGAAAGGTGTCAATTATGCAAGTTAGATGAAAGG
*
1285361 TTAAATACCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAAAAAGGTGTCAATTATG
66 TTAAATACCTTTGAGTAAAAGATTAATGGCCTAGATGTGCATTTGACAAAAAGGTGTCAATTATG
* *
1285426 CCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCTAGTTGTGCATTTGACAG
131 CCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCAAGCTGTGCATTTGACAG
1285491 AAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACC-TGAGC
196 AAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTGAGC
* *
1285537 AAAAGATTAATGGCCTAGTTATGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGG
1 AAAAGATTAATGGCCTAGCTATGCATTTGACAGAAAGGTGTCAATTATGCAAGTTAGATGAAAGG
*
1285602 TTAAATACCTTTGAGTAAAAGATTAATGGCCTAGATGTGCATTTGACAGAAAGGTGTCAATTATG
66 TTAAATACCTTTGAGTAAAAGATTAATGGCCTAGATGTGCATTTGACAAAAAGGTGTCAATTATG
* * * *
1285667 CCAGTTAGATGAAAGTTTAAATACCTTTGAGTAAAAGATTAATGGTCAAGCTGTGCATTTGGCAG
131 CCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCAAGCTGTGCATTTGACAG
*
1285732 AAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGT
196 AAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACC-TTGAGC
* * ** * * *
1285780 ACAAGATTAATGGCCTAGCTATGTATTTGGGAGGAATGTGTCAATCATGCAAGTTAGATGAAAGG
1 AAAAGATTAATGGCCTAGCTATGCATTTGACAGAAAGGTGTCAATTATGCAAGTTAGATGAAAGG
*
1285845 TTAAATACCTTTGGGTAAAAGA
66 TTAAATACCTTTGAGTAAAAGA
1285867 CAAAATGCTT
Statistics
Matches: 303, Mismatches: 25, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
241 222 0.73
243 81 0.27
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (242 bp):
AAAAGATTAATGGCCTAGCTATGCATTTGACAGAAAGGTGTCAATTATGCAAGTTAGATGAAAGG
TTAAATACCTTTGAGTAAAAGATTAATGGCCTAGATGTGCATTTGACAAAAAGGTGTCAATTATG
CCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATAGCCAAGCTGTGCATTTGACAG
AAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTGAGC
Found at i:1285962 original size:46 final size:46
Alignment explanation
Indices: 1285892--1285993 Score: 143
Period size: 46 Copynumber: 2.2 Consensus size: 46
1285882 TGCAATTTGA
* *
1285892 CATAAATG-AAATGCATAATGGTGCATAAAAGGCATGAGAGGATGC
1 CATAAATGAAAATGCATAACGGTGCATAAAAGGCATGAAAGGATGC
** * *
1285937 CATAAATGAAAATGTGTAACGGTGCATTAAAGGCATTAAAGGATGC
1 CATAAATGAAAATGCATAACGGTGCATAAAAGGCATGAAAGGATGC
1285983 CATAAATGAAA
1 CATAAATGAAA
1285994 TTAATGAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
45 8 0.16
46 42 0.84
ACGTcount: A:0.44, C:0.11, G:0.24, T:0.22
Consensus pattern (46 bp):
CATAAATGAAAATGCATAACGGTGCATAAAAGGCATGAAAGGATGC
Found at i:1297818 original size:2 final size:2
Alignment explanation
Indices: 1297811--1297853 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1297801 AATTACACGC
1297811 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
1297853 A
1 A
1297854 CACATTTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1299635 original size:5 final size:5
Alignment explanation
Indices: 1299625--1299709 Score: 68
Period size: 5 Copynumber: 17.0 Consensus size: 5
1299615 TAATTCCAAA
* * * *
1299625 AAAAT AAAAT AAAAT AAAAT AATAAA AGAAAT CAAAT GAAAT GAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AA-AAT A-AAAT AAAAT AAAAT AAAAT AAAAT
* *
1299677 AAAAT ATAAA- AATAT AAAA- GAAAT AAAA- AAAAT
1 AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT AAAAT
1299710 GTTAAGGTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
4 9 0.14
5 47 0.72
6 8 0.12
7 1 0.02
ACGTcount: A:0.75, C:0.01, G:0.05, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:1299661 original size:27 final size:26
Alignment explanation
Indices: 1299622--1299707 Score: 77
Period size: 27 Copynumber: 3.3 Consensus size: 26
1299612 GGATAATTCC
1299622 AAAAAAATAAAATAAAATAAAATAAT
1 AAAAAAATAAAATAAAATAAAATAAT
* * *
1299648 AAAAGAAATCAAATGAAATGAAATAA-
1 AAAA-AAATAAAATAAAATAAAATAAT
* * *
1299674 AATAAAATATAAA-AATATAAAAGAAAT
1 AAAAAAATA-AAATAAAATAAAA-TAAT
1299701 AAAAAAA
1 AAAAAAA
1299708 ATGTTAAGGT
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
25 10 0.22
26 12 0.26
27 24 0.52
ACGTcount: A:0.77, C:0.01, G:0.05, T:0.17
Consensus pattern (26 bp):
AAAAAAATAAAATAAAATAAAATAAT
Found at i:1300935 original size:3 final size:3
Alignment explanation
Indices: 1300907--1300961 Score: 58
Period size: 3 Copynumber: 17.3 Consensus size: 3
1300897 AAAAAAGTAA
*
1300907 AAT AA- AAT AAGT AAT AAT AGT AAAT AAT AAT AAT AAT AAT AAT AACT
1 AAT AAT AAT AA-T AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AA-T
1300954 ATAT AAT A
1 A-AT AAT A
1300962 TACATTTTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
2 2 0.04
3 33 0.73
4 9 0.20
5 1 0.02
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1301012 original size:43 final size:41
Alignment explanation
Indices: 1300982--1301269 Score: 129
Period size: 41 Copynumber: 6.9 Consensus size: 41
1300972 AAACTGTTTC
1300982 TTTT-AAAAACTATATATTATATATAAATTTTCAAAAATGT
1 TTTTAAAAAACTATATATTATATATAAATTTTCAAAAATGT
* * *
1301022 TTTTAAAAAACTATATAATT-TTTA-AAATGTTTTTAAAAACTATAT
1 TTTTAAAAAACTATAT-ATTATATATAAA---TTTTCAAAA--ATGT
** * **
1301067 AATTTTCAAAAATGTTTTAAAAACTATATATTATATATGTTTTC-AAAATGT
1 --TTTT-AAAAA---ACT--ATA-TAT-TA-TATATAAATTTTCAAAAATGT
* **
1301118 TTTTCAAAAACTATATATTATATATTTATTTTC-AAAATG-
1 TTTTAAAAAACTATATATTATATATAAATTTTCAAAAATGT
* * * *
1301157 TTTT-AAAAACTATATAATATATATATATTTCCAAGAAACCG-
1 TTTTAAAAAACTATATATTATATATAAATTTTCAA-AAA-TGT
*
1301198 TTTT-CAAAACTATATATTATATAT--ATTTT-AAAAATG-
1 TTTTAAAAAACTATATATTATATATAAATTTTCAAAAATGT
* * *
1301234 TTTTCAAAAACTATATA--ATATATACATTTTCGAAAA
1 TTTTAAAAAACTATATATTATATATAAATTTTCAAAAA
1301270 CCATTTTCTG
Statistics
Matches: 194, Mismatches: 27, Indels: 56
0.70 0.10 0.20
Matches are distributed among these distances:
35 6 0.03
36 5 0.03
37 19 0.10
38 31 0.16
39 9 0.05
40 27 0.14
41 39 0.20
42 6 0.03
43 10 0.05
45 4 0.02
47 4 0.02
48 9 0.05
49 4 0.02
51 4 0.02
53 7 0.04
54 6 0.03
56 3 0.02
57 1 0.01
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.44
Consensus pattern (41 bp):
TTTTAAAAAACTATATATTATATATAAATTTTCAAAAATGT
Found at i:1301064 original size:29 final size:30
Alignment explanation
Indices: 1301001--1301096 Score: 151
Period size: 29 Copynumber: 3.2 Consensus size: 30
1300991 CTATATATTA
1301001 TATATAAATTTTCAAAAATGTTTTTAAAAAAC
1 TATAT-AATTTTCAAAAATGTTTTT-AAAAAC
*
1301033 TATATAATTTT-TAAAATGTTTTTAAAAAC
1 TATATAATTTTCAAAAATGTTTTTAAAAAC
1301062 TATATAATTTTCAAAAATG-TTTTAAAAAC
1 TATATAATTTTCAAAAATGTTTTTAAAAAC
1301091 TATATA
1 TATATA
1301097 TTATATATGT
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
29 33 0.54
30 17 0.28
31 6 0.10
32 5 0.08
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (30 bp):
TATATAATTTTCAAAAATGTTTTTAAAAAC
Found at i:1301127 original size:38 final size:37
Alignment explanation
Indices: 1301062--1301269 Score: 244
Period size: 38 Copynumber: 5.5 Consensus size: 37
1301052 TTTTAAAAAC
1301062 TATATA-ATTTTCAAAAATGTTTT-AAAAACTATATAT
1 TATATATATTTTC-AAAATGTTTTCAAAAACTATATAT
*
1301098 TATATATGTTTTCAAAATGTTTTTCAAAAACTATATAT
1 TATATATATTTTCAAAATG-TTTTCAAAAACTATATAT
1301136 TATATATTTATTTTCAAAATGTTTT-AAAAACTATATAAT
1 TATATA--TATTTTCAAAATGTTTTCAAAAACTATAT-AT
* *
1301175 ATATATATATTTCCAAGAAACCGTTTTC-AAAACTATATAT
1 -TATATATATTTTC-A-AAA-TGTTTTCAAAAACTATATAT
* *
1301215 TATATATATTTTAAAAATGTTTTCAAAAACTATATAA
1 TATATATATTTTCAAAATGTTTTCAAAAACTATATAT
*
1301252 TATATACATTTTCGAAAA
1 TATATATATTTTC-AAAA
1301270 CCATTTTCTG
Statistics
Matches: 149, Mismatches: 10, Indels: 24
0.81 0.05 0.13
Matches are distributed among these distances:
36 18 0.12
37 34 0.23
38 41 0.28
39 18 0.12
40 23 0.15
41 15 0.10
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (37 bp):
TATATATATTTTCAAAATGTTTTCAAAAACTATATAT
Found at i:1303198 original size:2 final size:2
Alignment explanation
Indices: 1303191--1303226 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1303181 ACAAAATTGA
1303191 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
1303227 TTATTGCATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1306983 original size:23 final size:23
Alignment explanation
Indices: 1306957--1307002 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
1306947 ATGTTTTAAT
1306957 TGACGT-GCAGTGGTGCATGTCCA
1 TGACGTGGC-GTGGTGCATGTCCA
1306980 TGACGTGGCGTGGTGCATGTCCA
1 TGACGTGGCGTGGTGCATGTCCA
1307003 ACCTAGAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.15, C:0.22, G:0.37, T:0.26
Consensus pattern (23 bp):
TGACGTGGCGTGGTGCATGTCCA
Found at i:1307715 original size:6 final size:6
Alignment explanation
Indices: 1307704--1307752 Score: 98
Period size: 6 Copynumber: 8.2 Consensus size: 6
1307694 ACTTTGGCAT
1307704 ATTCCC ATTCCC ATTCCC ATTCCC ATTCCC ATTCCC ATTCCC ATTCCC
1 ATTCCC ATTCCC ATTCCC ATTCCC ATTCCC ATTCCC ATTCCC ATTCCC
1307752 A
1 A
1307753 GCCTAATCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.18, C:0.49, G:0.00, T:0.33
Consensus pattern (6 bp):
ATTCCC
Found at i:1314674 original size:61 final size:60
Alignment explanation
Indices: 1314605--1314729 Score: 232
Period size: 61 Copynumber: 2.1 Consensus size: 60
1314595 ACGGCTTTAA
*
1314605 TCAATCCCTAACGGATCCAAAAGGCTAGATTAATATTAAAAGATATAAAAAAGACCAAAAT
1 TCAATCCCTAACGGATCCAAAAGGCTAAATTAATATTAAAAGATAT-AAAAAGACCAAAAT
1314666 TCAATCCCTAACGGATCCAAAAGGCTAAATTAATATTAAAAGATATAAAAAGACCAAAAT
1 TCAATCCCTAACGGATCCAAAAGGCTAAATTAATATTAAAAGATATAAAAAGACCAAAAT
1314726 TCAA
1 TCAA
1314730 ATGAAGAACA
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
60 18 0.29
61 45 0.71
ACGTcount: A:0.51, C:0.17, G:0.10, T:0.22
Consensus pattern (60 bp):
TCAATCCCTAACGGATCCAAAAGGCTAAATTAATATTAAAAGATATAAAAAGACCAAAAT
Found at i:1314957 original size:29 final size:29
Alignment explanation
Indices: 1314915--1314974 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
1314905 TAAGTTTTCG
**
1314915 TTTGTAAATTTAGTGGATTTGAAAAATCT
1 TTTGTAAATTTAGTAAATTTGAAAAATCT
*
1314944 TTTGTAAATTTAGTAAATTTGAGAAATCT
1 TTTGTAAATTTAGTAAATTTGAAAAATCT
1314973 TT
1 TT
1314975 GTTGTGAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (29 bp):
TTTGTAAATTTAGTAAATTTGAAAAATCT
Found at i:1315300 original size:38 final size:37
Alignment explanation
Indices: 1315206--1315311 Score: 98
Period size: 38 Copynumber: 2.9 Consensus size: 37
1315196 TCGGGTCGAG
* * *
1315206 TATATATATATTTA-AATTAAATATATAAATATTATA
1 TATATATATATTAATAATTAAATTTATTAATATTATA
*
1315242 TATAT-T-TTTTAATTTAAATTAAATTTATTAATATTATA
1 TATATATATATTAA--T-AATTAAATTTATTAATATTATA
1315280 TATATATATATATAATAATT--ATTT-TTAATATT
1 TATATATATAT-TAATAATTAAATTTATTAATATT
1315312 TATCGGGTCG
Statistics
Matches: 58, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
34 4 0.07
35 9 0.16
36 9 0.16
38 29 0.50
39 2 0.03
40 2 0.03
41 3 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (37 bp):
TATATATATATTAATAATTAAATTTATTAATATTATA
Found at i:1315409 original size:35 final size:36
Alignment explanation
Indices: 1315363--1315436 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 36
1315353 ATCAAACCCA
*
1315363 TCCCCGTCCCCGTTTAACATAAA-TGATTTTCCCCG
1 TCCCCGTCCCCGTTTAACATAAACGGATTTTCCCCG
* *
1315398 TCCCCGTCCCCGTTTAGCATAAACGGGTTTTCCCCG
1 TCCCCGTCCCCGTTTAACATAAACGGATTTTCCCCG
1315434 TCC
1 TCC
1315437 TTGTTTAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
35 22 0.63
36 13 0.37
ACGTcount: A:0.16, C:0.39, G:0.15, T:0.30
Consensus pattern (36 bp):
TCCCCGTCCCCGTTTAACATAAACGGATTTTCCCCG
Found at i:1315781 original size:21 final size:22
Alignment explanation
Indices: 1315757--1315807 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1315747 CATACAACTA
1315757 AAAT-AATAAAT-TATTTAAAAT
1 AAATCAATAAATAT-TTTAAAAT
**
1315778 AAATCAATCTATATTTTAAAAT
1 AAATCAATAAATATTTTAAAAT
1315800 AAATCAAT
1 AAATCAAT
1315808 CCATACTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 4 0.15
22 21 0.81
23 1 0.04
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (22 bp):
AAATCAATAAATATTTTAAAAT
Found at i:1315821 original size:22 final size:22
Alignment explanation
Indices: 1315772--1315820 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1315762 ATAAATTATT
* **
1315772 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCCATATAA
1315794 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
1315817 TAAA
1 TAAA
1315821 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1315824 original size:54 final size:54
Alignment explanation
Indices: 1315760--1316223 Score: 757
Period size: 54 Copynumber: 8.4 Consensus size: 54
1315750 ACAACTAAAA
*
1315760 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* *
1315814 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATAAATCCATGC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
1315868 TAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAACAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATCAATCCATAC
*
1315932 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
1315986 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1316040 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
1316094 TAATAAATTATTTAAAATAAATCAATCCATAATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
1316148 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
*
1316202 AAATAAATTATTTAAAATAAAT
1 TAATAAATTATTTAAAATAAAT
1316224 TATTTTAAAA
Statistics
Matches: 385, Mismatches: 15, Indels: 20
0.92 0.04 0.05
Matches are distributed among these distances:
54 328 0.85
55 2 0.01
56 1 0.00
58 3 0.01
60 3 0.01
62 1 0.00
63 2 0.01
64 45 0.12
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:1315830 original size:32 final size:32
Alignment explanation
Indices: 1315792--1316223 Score: 390
Period size: 32 Copynumber: 15.4 Consensus size: 32
1315782 CAATCTATAT
1315792 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1315824 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
1315846 TTTAAAATAAATAAATCCATGCTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1315878 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
1315910 TTTAAAACAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1315942 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
1315964 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1315996 TTTAAAATAAATC-A---AT-CT-AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1316018 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1316050 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1316072 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1316104 TTTAAAATAAATCAAT-C---C--AT--A--A
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1316126 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1316158 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
1316180 TTTAAAATAAATCAATCTATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1316212 TTTAAAATAAAT
1 TTTAAAATAAAT
1316224 TATTTTAAAA
Statistics
Matches: 333, Mismatches: 7, Indels: 120
0.72 0.02 0.26
Matches are distributed among these distances:
22 93 0.28
23 9 0.03
24 6 0.02
26 19 0.06
27 4 0.01
28 19 0.06
30 6 0.02
31 11 0.03
32 166 0.50
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:1315850 original size:22 final size:22
Alignment explanation
Indices: 1315824--1315865 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1315814 TAATAAATTA
*
1315824 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATAAATCCATAT
1315846 TTTAAAATAAATAAATCCAT
1 TTTAAAATAAATAAATCCAT
1315866 GCTAATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (22 bp):
TTTAAAATAAATAAATCCATAT
Found at i:1315993 original size:22 final size:22
Alignment explanation
Indices: 1315944--1315992 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1315934 ATAAATTATT
**
1315944 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
1315966 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
1315989 TAAA
1 TAAA
1315993 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1316022 original size:22 final size:22
Alignment explanation
Indices: 1315996--1316038 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1315986 TAATAAATTA
*
1315996 TTTAAAATAAATCAATCTATAT
1 TTTAAAATAAATCAATCCATAT
1316018 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
1316039 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1316047 original size:22 final size:22
Alignment explanation
Indices: 1315998--1316046 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1315988 ATAAATTATT
* **
1315998 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCCATATAA
1316020 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
1316043 TAAA
1 TAAA
1316047 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1316076 original size:22 final size:22
Alignment explanation
Indices: 1316050--1316092 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1316040 TAATAAATTA
1316050 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
1316072 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
1316093 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1316101 original size:22 final size:22
Alignment explanation
Indices: 1316052--1316154 Score: 71
Period size: 22 Copynumber: 4.2 Consensus size: 22
1316042 ATAAATTATT
**
1316052 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
1316074 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
* *
1316097 TAAATTATTTAAAATAAATCAATCCATAA
1 TAAA--A--T-AAATCAATCCAT--ATAA
1316126 TTTAAAATAAATCAATCCATACTAA
1 --TAAAATAAATCAATCCATA-TAA
1316151 TAAA
1 TAAA
1316155 TTATTTAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 21
0.70 0.07 0.23
Matches are distributed among these distances:
22 19 0.30
23 9 0.14
24 1 0.02
25 4 0.06
26 10 0.16
27 2 0.03
28 10 0.16
29 4 0.06
30 1 0.02
31 4 0.06
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1316184 original size:22 final size:22
Alignment explanation
Indices: 1316158--1316258 Score: 85
Period size: 22 Copynumber: 4.5 Consensus size: 22
1316148 TAATAAATTA
1316158 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
* *
1316180 TTTAAAATAAATCAATCTATACA
1 TTTAAAATAAATCAATCCATA-T
** * ** * **
1316203 AATAAATTATTTAAAATAAATTAT
1 TTTAAAATAAAT-CAATCCA-TAT
1316227 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
1316249 TTTAAAATAA
1 TTTAAAATAA
1316259 TTTATTTTAA
Statistics
Matches: 57, Mismatches: 19, Indels: 6
0.70 0.23 0.07
Matches are distributed among these distances:
22 33 0.58
23 11 0.19
24 11 0.19
25 2 0.04
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1316219 original size:14 final size:15
Alignment explanation
Indices: 1316177--1316275 Score: 74
Period size: 15 Copynumber: 6.0 Consensus size: 15
1316167 AATCAATCCA
1316177 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
* *
1316192 CAATCTATACAAATAAAT
1 -TAT-TTTA-AAATAAAT
1316210 TA-TTTAAAATAAAT
1 TATTTTAAAATAAAT
1316224 TATTTTAAAATAAATCAAT
1 TATTTTAAAAT--A--AAT
*
1316243 CCATATTTTAAAATAATT
1 ---TATTTTAAAATAAAT
1316261 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
1316276 AACCTTATTA
Statistics
Matches: 67, Mismatches: 6, Indels: 21
0.71 0.06 0.22
Matches are distributed among these distances:
14 10 0.15
15 25 0.37
16 2 0.03
17 5 0.07
18 10 0.15
19 3 0.04
20 1 0.01
22 11 0.16
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (15 bp):
TATTTTAAAATAAAT
Found at i:1325486 original size:97 final size:97
Alignment explanation
Indices: 1325320--1325513 Score: 325
Period size: 97 Copynumber: 2.0 Consensus size: 97
1325310 ATATTGTTCC
* *
1325320 TTATTTATTGGATTCCTATATTTTCTTAACTTCAAATTTGCTTCCATGGGAGTTTTCGAAGGCTT
1 TTATTTACTGGATTCCTATATTTTCTTAACTTCAAATTTGCTTCCATGAGAGTTTTCGAAGGCTT
* * *
1325385 GCAACCAGTCATTTTGGTTTCGGAGAGTAAAT
66 GCAACCAATCATTCTGGTTTCAGAGAGTAAAT
*
1325417 TTATTTACTGGATTCCTATATTTTCTTAACTTCAAATTTGTTTCCATGAGAGTTTTCGAAGGCTT
1 TTATTTACTGGATTCCTATATTTTCTTAACTTCAAATTTGCTTCCATGAGAGTTTTCGAAGGCTT
*
1325482 GCAACCAATTATTCTGGTTTCAGAGAGTAAAT
66 GCAACCAATCATTCTGGTTTCAGAGAGTAAAT
1325514 CCATAATGTA
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
97 90 1.00
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.42
Consensus pattern (97 bp):
TTATTTACTGGATTCCTATATTTTCTTAACTTCAAATTTGCTTCCATGAGAGTTTTCGAAGGCTT
GCAACCAATCATTCTGGTTTCAGAGAGTAAAT
Found at i:1330980 original size:32 final size:32
Alignment explanation
Indices: 1330929--1330989 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
1330919 AACTATTTTT
* *
1330929 CATTATCTAATTGTAACTCTAACTCGACTTGG
1 CATTATCCAAATGTAACTCTAACTCGACTTGG
* * *
1330961 CATTATCCAAATGTGACTCTGACTTGACT
1 CATTATCCAAATGTAACTCTAACTCGACT
1330990 GTGTACTATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (32 bp):
CATTATCCAAATGTAACTCTAACTCGACTTGG
Found at i:1331197 original size:15 final size:15
Alignment explanation
Indices: 1331177--1331206 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1331167 ACCTGCCAAC
1331177 CCACCCCTCGCAAGT
1 CCACCCCTCGCAAGT
1331192 CCACCCCTCGCAAGT
1 CCACCCCTCGCAAGT
1331207 ATTAATGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.53, G:0.13, T:0.13
Consensus pattern (15 bp):
CCACCCCTCGCAAGT
Found at i:1335412 original size:32 final size:32
Alignment explanation
Indices: 1335371--1335432 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
1335361 ACTGTAACTG
* *
1335371 CTTGACATTATCTAATTGCAACTCTAACTCGA
1 CTTGACATTATCCAAATGCAACTCTAACTCGA
* * *
1335403 CTTGGCATTATCCAAATGTAGCTCTAACTC
1 CTTGACATTATCCAAATGCAACTCTAACTC
1335433 TGCTGTGTAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (32 bp):
CTTGACATTATCCAAATGCAACTCTAACTCGA
Found at i:1339746 original size:32 final size:31
Alignment explanation
Indices: 1339671--1339747 Score: 75
Period size: 32 Copynumber: 2.4 Consensus size: 31
1339661 TACTTTACAT
*
1339671 TATCTAATTGCAACTCTAACTCAACTTGGTAT
1 TATCTAA-TGCAACTCTAACTCAACTTGGTAG
* **
1339703 TATCCAAATGCAACTCTAACTC-TGTTGTGTAG
1 TAT-CTAATGCAACTCTAACTCAACTTG-GTAG
1339735 TATCTATATGCAA
1 TATCTA-ATGCAA
1339748 TGTTGACTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
31 5 0.14
32 29 0.78
33 3 0.08
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (31 bp):
TATCTAATGCAACTCTAACTCAACTTGGTAG
Found at i:1347253 original size:16 final size:16
Alignment explanation
Indices: 1347232--1347264 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1347222 TAATAAATAA
1347232 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1347248 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1347264 A
1 A
1347265 AATTGTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1347355 original size:16 final size:16
Alignment explanation
Indices: 1347334--1347378 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
1347324 TAATAAATAA
*
1347334 ACGAACAAAAACGAAC
1 ACGAACATAAACGAAC
*
1347350 ACGAACTTAAACGAAC
1 ACGAACATAAACGAAC
1347366 ACGAACATAAACG
1 ACGAACATAAACG
1347379 TTGAAGACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.56, C:0.24, G:0.13, T:0.07
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1352955 original size:14 final size:14
Alignment explanation
Indices: 1352938--1352983 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
1352928 AATGAACATA
*
1352938 AACGAACATAACCG
1 AACGAACATAAACG
1352952 AACGAACATAAACG
1 AACGAACATAAACG
*
1352966 AACGAACATAATCG
1 AACGAACATAAACG
1352980 AACG
1 AACG
1352984 TTCACGAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.52, C:0.24, G:0.15, T:0.09
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:1352981 original size:24 final size:24
Alignment explanation
Indices: 1352931--1352982 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1352921 ATAAATGAAT
* *
1352931 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACAGAACAGAAC
*
1352955 GAACATAAACGAAC-GAACATAATC
1 GAACATAAACGAACAGAACAGAA-C
1352979 GAAC
1 GAAC
1352983 GTTCACGAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.54, C:0.23, G:0.13, T:0.10
Consensus pattern (24 bp):
GAACATAAACGAACAGAACAGAAC
Found at i:1352992 original size:38 final size:39
Alignment explanation
Indices: 1352918--1353008 Score: 98
Period size: 38 Copynumber: 2.4 Consensus size: 39
1352908 GATTGGATTA
* *
1352918 AACATAAATGAATGAACATAAACGAACATAACCGAACG-
1 AACATAAACGAACGAACATAAACGAACATAACCGAACGT
* * *
1352956 AACATAAACGAACGAACATAATCGAACGT-TCACGAACGT
1 AACATAAACGAACGAACATAAACGAACATAAC-CGAACGT
*
1352995 AA-ATGAACGAACGA
1 AACATAAACGAACGA
1353009 GACCTATGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
37 1 0.02
38 42 0.93
39 2 0.04
ACGTcount: A:0.52, C:0.20, G:0.15, T:0.13
Consensus pattern (39 bp):
AACATAAACGAACGAACATAAACGAACATAACCGAACGT
Found at i:1354763 original size:30 final size:30
Alignment explanation
Indices: 1354727--1354788 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1354717 ATACCTAATT
1354727 CTAAAAATCTATTTATAGCCAATCACCTTA
1 CTAAAAATCTATTTATAGCCAATCACCTTA
1354757 CTAAAAATCTATTTATAGCCAATCACCTTA
1 CTAAAAATCTATTTATAGCCAATCACCTTA
1354787 CT
1 CT
1354789 TTCGGAAGGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.39, C:0.24, G:0.03, T:0.34
Consensus pattern (30 bp):
CTAAAAATCTATTTATAGCCAATCACCTTA
Found at i:1358838 original size:18 final size:18
Alignment explanation
Indices: 1358770--1358833 Score: 101
Period size: 18 Copynumber: 3.6 Consensus size: 18
1358760 AGGGATTATC
1358770 AGTGGTCCTTCGAGACAT
1 AGTGGTCCTTCGAGACAT
*
1358788 AGTGGTCCTTTGAGACAT
1 AGTGGTCCTTCGAGACAT
* *
1358806 AGTGGTTCTTCGGGACAT
1 AGTGGTCCTTCGAGACAT
1358824 AGTGGTCCTT
1 AGTGGTCCTT
1358834 TGGGAAAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.33
Consensus pattern (18 bp):
AGTGGTCCTTCGAGACAT
Found at i:1364925 original size:18 final size:18
Alignment explanation
Indices: 1364895--1364945 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
1364885 GGATTATCAA
1364895 TGGT-CTTTCGGGACATAG
1 TGGTCCTTT-GGGACATAG
*
1364913 TGGTCCTTTGGGATATAG
1 TGGTCCTTTGGGACATAG
*
1364931 TGGTCATTTGGGACA
1 TGGTCCTTTGGGACA
1364946 AATATTTAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 25 0.86
19 4 0.14
ACGTcount: A:0.18, C:0.14, G:0.33, T:0.35
Consensus pattern (18 bp):
TGGTCCTTTGGGACATAG
Found at i:1365652 original size:13 final size:13
Alignment explanation
Indices: 1365634--1365658 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1365624 TGCTGCTGTT
1365634 TTTTTTTCTTCTA
1 TTTTTTTCTTCTA
1365647 TTTTTTTCTTCT
1 TTTTTTTCTTCT
1365659 TTTATGAAGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTTTCTTCTA
Found at i:1370347 original size:22 final size:21
Alignment explanation
Indices: 1370322--1370378 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
1370312 GGGGGTTTGG
1370322 TAAAAAGATATTTAAGTAATAA
1 TAAAAAGATATTTAAGTAA-AA
*
1370344 TAAAAATGAT-TTAAAGTAAAA
1 TAAAAA-GATATTTAAGTAAAA
*
1370365 TAAAGAAAATATTT
1 TAAA-AAGATATTT
1370379 TAAAGTTGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 8 0.28
22 18 0.62
23 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.32
Consensus pattern (21 bp):
TAAAAAGATATTTAAGTAAAA
Found at i:1372448 original size:2 final size:2
Alignment explanation
Indices: 1372441--1372479 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1372431 CTAATCATAA
1372441 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1372480 GAGCAAAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1373349 original size:51 final size:49
Alignment explanation
Indices: 1373294--1373407 Score: 133
Period size: 51 Copynumber: 2.2 Consensus size: 49
1373284 TCCCTGCCAT
** *
1373294 GCGCTATATGCTGATTTGGC-ACCACGTGTGGTATAGCGCGCCCCCTG-TACC
1 GCGCTATA-GCTGACATGGCGA-CACGTG-GGTATAGCGCACCCCCTGAT-CC
1373345 GCGCTATACGCTGACATGGCGTACACGTGGGTATAGCGCACCCCCTGATCC
1 GCGCTATA-GCTGACATGGCG-ACACGTGGGTATAGCGCACCCCCTGATCC
1373396 GCGCTATAGCTG
1 GCGCTATAGCTG
1373408 TTTATCTGAC
Statistics
Matches: 56, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
50 4 0.07
51 44 0.79
52 7 0.12
53 1 0.02
ACGTcount: A:0.18, C:0.32, G:0.28, T:0.23
Consensus pattern (49 bp):
GCGCTATAGCTGACATGGCGACACGTGGGTATAGCGCACCCCCTGATCC
Found at i:1378943 original size:23 final size:23
Alignment explanation
Indices: 1378899--1378945 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
1378889 AACATATTAA
**
1378899 GTAGCGCTTATATAATGTAATAG
1 GTAGCGCTTATATAATAAAATAG
1378922 GTAGCGCTTATATAATAAAATAG
1 GTAGCGCTTATATAATAAAATAG
1378945 G
1 G
1378946 CATTTAACCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (23 bp):
GTAGCGCTTATATAATAAAATAG
Found at i:1379005 original size:87 final size:87
Alignment explanation
Indices: 1378859--1379021 Score: 245
Period size: 87 Copynumber: 1.9 Consensus size: 87
1378849 TATCTTATAT
* *
1378859 CATTTAACCGAAAATATTATCAAGCACAATAACATATTAAGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCGAAAATATTATCAAGCACAATAACATATTAAGTAACACTTATATAATGTAATAGGT
1378924 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
** * * * * *
1378946 CATTTAACCGGTAATATTATTAAGTATAATAACATATTAGGTAACACTTATATAATGTAATATGT
1 CATTTAACCGAAAATATTATCAAGCACAATAACATATTAAGTAACACTTATATAATGTAATAGGT
1379011 AGCGCTTATAT
66 AGCGCTTATAT
1379022 TGACCTATTT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 67 1.00
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.34
Consensus pattern (87 bp):
CATTTAACCGAAAATATTATCAAGCACAATAACATATTAAGTAACACTTATATAATGTAATAGGT
AGCGCTTATATAATAAAATAGG
Found at i:1379588 original size:20 final size:20
Alignment explanation
Indices: 1379563--1379614 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1379553 AGCGTTTTAC
*
1379563 CGGTTTTGTCATTTTAAGAT
1 CGGTTTTGTCATTTTAAGAA
*
1379583 CGGTTTTGTCATTTTGAGAA
1 CGGTTTTGTCATTTTAAGAA
*
1379603 CGATTTTGTCAT
1 CGGTTTTGTCAT
1379615 ATTTTTACCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.19, C:0.12, G:0.21, T:0.48
Consensus pattern (20 bp):
CGGTTTTGTCATTTTAAGAA
Found at i:1379988 original size:20 final size:19
Alignment explanation
Indices: 1379940--1379988 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
1379930 ATCCGGTATC
**
1379940 TTTTTACCGGTTTTGTCAT
1 TTTTTACCTCTTTTGTCAT
*
1379959 TTTTAGACCTCTTTTGTCAT
1 TTTT-TACCTCTTTTGTCAT
1379979 ATTTTTACCT
1 -TTTTTACCT
1379989 GTTATATTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 4 0.17
20 16 0.67
21 4 0.17
ACGTcount: A:0.14, C:0.18, G:0.10, T:0.57
Consensus pattern (19 bp):
TTTTTACCTCTTTTGTCAT
Found at i:1380117 original size:182 final size:182
Alignment explanation
Indices: 1379583--1381085 Score: 1165
Period size: 182 Copynumber: 8.1 Consensus size: 182
1379573 ATTTTAAGAT
* * *
1379583 CGGTTTTGTCATTTTGAGAACGATTTTGTCATATTTTTACCTGTTATATTATTATGGATCGATAC
1 CGGTTTTGTCATTTTGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATAC
* * * *
1379648 ATTTTTTTTAAAGTATCGACACTTTATAGGTGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTG
66 A-TTTTTATAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTTCAAAAGTG
*
1379713 TCGATACTTATATTAAAGTATCGACACTTTCAACATATTCGGTAGTTATTTAC
130 TCGATACTTATATTAAAGTATCGACACTTTCAACATATCCGGTAGTTATTTAC
* * * * *
1379766 CTGTTTTGTGATTTTGAGACCAGATTTGTCATATTTTTAGCTGTTATATTGTTATGGATCGATAC
1 CGGTTTTGTCATTTTGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATAC
* * *
1379831 ATTTTCATAAAGTGTCGACACTTTTTAGGCGC-ATAACTTTTTCTCTTTTAAA-TTCTAAAAGTG
66 ATTTTTATAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTTC-AAAAGTG
* *
1379894 TCGATACTTATATTAAATTATCGACACTTTCAACATATCCGGTA-TCTTTTTAC
130 TCGATACTTATATTAAAGTATCGACACTTTCAACATATCCGGTAGT-TATTTAC
* ** *
1379947 CGGTTTTGTCATTTTTAGACCTCTTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGATAC
1 CGGTTTTGTCATTTTGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATAC
*
1380012 ATTTTT-TAAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTTCAAAAGTG
66 ATTTTTAT-AAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTTCAAAAGTG
*
1380076 TCGATACTTATATTAAAGTATCGACACTTTAAACATATCCGGTAGTTATTTAC
130 TCGATACTTATATTAAAGTATCGACACTTTCAACATATCCGGTAGTTATTTAC
** * * ** * * ***
1380129 ATGTTTTGTCATTTTTAGACCGATTTTGTCAT-TTTGAGACC-GGT-T-TTGTCAT--ATTTTTA
1 CGGTTTTGTCATTTTGAGACCGGTTTTGTCATATTT-TTACCTGTTATATTGTTATGGATCGATA
* * * * * * * ** * * ****
1380188 GC-TGTTATATAGTTATGGATCGATACATTTT---C-ATA-AAGTGTCGACACTTTTTAGGCGCT
65 -CAT-TT-T-TA-TAAAGTATCGACACTTTTTAGGCGCTATAACT-TCTTCTCTTTTAAATTTC-
* * * * * * * * ** *
1380247 ATAACT-TC-TTCTCTTTTAAATTCAGAAAGTGTCGATACTTAT-ATTAAATTAT-CGACACTT-
123 AAAAGTGTCGAT-AC--TTATATT---AAAGTATCGACACTT-TCA--ACA-TATCCGGTAGTTA
1380307 TTAACATATC
178 TT----TA-C
* * ** * * * * ** *
1380317 CGG--TAG-CGTTTT---ACCGGTTTTGTCAT-TTTGAGACCGGTTTTGTCATATT-TTTACCTG
1 CGGTTTTGTCATTTTGAGACCGGTTTTGTCATATTT-TTACCTGTTATAT--TGTTATGGATC-G
* * * ** **
1380374 TTATATTGTTATGAATCGATACATTTTTTTAAAGTATCGACACTTTATAGGCGCTATAACTTCTT
62 ATACATT-TT-T--AT--A-A-A-----GTATCG-A-C-ACTTTT--TAGGCGCTATAACTTCTT
* * *
1380439 CTCTTTTAAATTCCAAAAGTGTCGATAATTATATTAAAGTATCGATACTTTCAACATATCCGGTA
109 CTCTTTTAAATTTCAAAAGTGTCGATACTTATATTAAAGTATCGACACTTTCAACATATCCGGTA
1380504 GTTATTTAC
174 GTTATTTAC
* **
1380513 CTGTTTTGTCATTTTGAGACCGGTTTTGTCATATTTTTAGATGTTATATTGTTATGGATCGATAC
1 CGGTTTTGTCATTTTGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATAC
* * * *
1380578 ATTTTCATAAAGTGTCGACACTTTTTAGACACTATAACTTCTTCTCTTTTAAA-TTCAGAAAGTG
66 ATTTTTATAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTTCA-AAAGTG
* * * * *
1380642 TCGATACTTATATTAAATTCTAGACACTTTCAACATATCTGATAGTGT-TTTAC
130 TCGATACTTATATTAAAGTATCGACACTTTCAACATATCCGGTAGT-TATTTAC
** *
1380695 CGGTTTTGTCATTTTGAGACATGTTTTGTCATATTTTTACATGTTAACAATATATTGTTATGGAT
1 CGGTTTTGTCATTTTGAGACCGGTTTTGTCATATTTTTACCTG-T-----TATATTGTTATGGAT
* *
1380760 CGATACATTTTTTTAAAGTATCGACA-TTTTATAGGCGCTATAA---CTTCTCTTTTAAATTCCA
60 CGATACATTTTTATAAAGTATCGACACTTTT-TAGGCGCTATAACTTCTTCTCTTTTAAATTTCA
* *
1380821 AAAGTGTCGATAATTATATTAAAGTATCGACACTTTCAACATATTCGGTAGTTATTTAC
124 AAAGTGTCGATACTTATATTAAAGTATCGACACTTTCAACATATCCGGTAGTTATTTAC
* * *
1380880 CTGTTTTGTCATTTTGAGACCAGTTTTGTCATATTTTTAGCTGTTATATTGTTATGGATCGATAC
1 CGGTTTTGTCATTTTGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATAC
* * * ** *
1380945 ATTTTCATAAAGTTTCAACTTTTTTTAGGCGTTATAACTTCTTCTCTTTTAAA-TTCAGAAAGTG
66 ATTTTTATAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTTCA-AAAGTG
* * * *
1381009 TCGATTCTTATATTAAATTATCGACACTTTCAACATATCTGGTAG-CATTTTAC
130 TCGATACTTATATTAAAGTATCGACACTTTCAACATATCCGGTAGTTA-TTTAC
*
1381062 C-GTTTTGTTATTTTGAGACCGGTT
1 CGGTTTTGTCATTTTGAGACCGGTT
1381086 ATATTGTTAT
Statistics
Matches: 1047, Mismatches: 182, Indels: 184
0.74 0.13 0.13
Matches are distributed among these distances:
176 4 0.00
177 20 0.02
178 8 0.01
179 60 0.06
180 10 0.01
181 203 0.19
182 348 0.33
183 69 0.07
184 14 0.01
185 111 0.11
186 7 0.01
187 10 0.01
188 55 0.05
189 6 0.01
190 1 0.00
192 2 0.00
193 1 0.00
194 1 0.00
196 5 0.00
197 2 0.00
198 4 0.00
199 11 0.01
200 16 0.02
201 11 0.01
202 35 0.03
203 4 0.00
205 6 0.01
206 5 0.00
207 14 0.01
208 4 0.00
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (182 bp):
CGGTTTTGTCATTTTGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATAC
ATTTTTATAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTTCAAAAGTGT
CGATACTTATATTAAAGTATCGACACTTTCAACATATCCGGTAGTTATTTAC
Found at i:1380157 original size:20 final size:20
Alignment explanation
Indices: 1380132--1380185 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
1380122 TATTTACATG
1380132 TTTTGTCATTTTTAGACCGA
1 TTTTGTCATTTTTAGACCGA
* *
1380152 TTTTGTCATTTTGAGACCGG
1 TTTTGTCATTTTTAGACCGA
1380172 TTTTGTCATATTTT
1 TTTTGTCAT-TTTT
1380186 TAGCTGTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 27 0.90
21 3 0.10
ACGTcount: A:0.17, C:0.13, G:0.17, T:0.54
Consensus pattern (20 bp):
TTTTGTCATTTTTAGACCGA
Found at i:1380253 original size:384 final size:363
Alignment explanation
Indices: 1379583--1381081 Score: 2265
Period size: 364 Copynumber: 4.1 Consensus size: 363
1379573 ATTTTAAGAT
* *
1379583 CGGTTTTGTCATTTTGAGAAC-GATTTTGTCATATTTTTACCTGTTATATTATTATGGATCGATA
1 CGGTTTTGTCATTTTGAGACCTG-TTTTGTCATATTTTTACCTGTTATATTGTTAT-GATCGATA
*
1379647 CATTTTTTTTAAAGTATCGACACTTTATAGGTGCTATAACTTCTTCTCTTTTAAATTCCAAAAGT
64 CA-TTTTTTTAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGT
* * *
1379712 GTCGATACTTATATTAAAGTATCGACACTTTCAACATATTCGGTAGTTATTTACCTGTTTTGTGA
128 GTCGATAATTATATTAAAGTATCGACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCA
*
1379777 TTTTGAGACCAGATTTGTCATATTTTTAGCTGTTATATTGTTATGGATCGATACATTTTCATAAA
193 TTTTGAGACCAGTTTTGTCATATTTTTAGCTGTTATATTGTTATGGATCGATACATTTTCATAAA
*
1379842 GTGTCGACACTTTTTAGGCGC-ATAACTTTTTCTCTTTTAAATTCTA-AAAGTGTCGATACTTAT
258 GTGTCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTC-AGAAAGTGTCGATACTTAT
* *
1379905 ATTAAATTATCGACACTTTCAACATATCCGGTATCTTTTTAC
322 ATTAAATTATCGACACTTTCAACATATCCGGTAGCGTTTTAC
* *
1379947 CGGTTTTGTCATTTTTAGACCTCTTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGATAC
1 CGGTTTTGTCATTTTGAGACCTGTTTTGTCATATTTTTACCTGTTATATTGTTAT-GATCGATAC
* *
1380012 ATTTTTTAAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTTCAAAAGTGT
65 ATTTTTTTAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGT
* *
1380077 CGATACTTATATTAAAGTATCGACACTTTAAACATATCCGGTAGTTATTTACATGTTTTGTCATT
130 CGATAATTATATTAAAGTATCGACACTTTCAACATATCCGGTAGTTATTTAC---------C---
* *
1380142 TTTAGACCGATTTTGTCATTTTGAGACCGGTTTTGTCATATTTTTAGCTGTTATATAGTTATGGA
183 --T-----G-TTTTGTCATTTTGAGACCAGTTTTGTCATATTTTTAGCTGTTATATTGTTATGGA
1380207 TCGATACATTTTCATAAAGTGTCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAG
240 TCGATACATTTTCATAAAGTGTCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAG
*
1380272 AAAGTGTCGATACTTATATTAAATTATCGACACTTTTAACATATCCGGTAGCGTTTTAC
305 AAAGTGTCGATACTTATATTAAATTATCGACACTTTCAACATATCCGGTAGCGTTTTAC
*
1380331 CGGTTTTGTCATTTTGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGAATCGATAC
1 CGGTTTTGTCATTTTGAGACCTGTTTTGTCATATTTTTACCTGTTATATTGTTATG-ATCGATAC
1380396 ATTTTTTTAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGT
65 ATTTTTTTAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGT
*
1380461 CGATAATTATATTAAAGTATCGATACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATT
130 CGATAATTATATTAAAGTATCGACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATT
* *
1380526 TTGAGACCGGTTTTGTCATATTTTTAGATGTTATATTGTTATGGATCGATACATTTTCATAAAGT
195 TTGAGACCAGTTTTGTCATATTTTTAGCTGTTATATTGTTATGGATCGATACATTTTCATAAAGT
* *
1380591 GTCGACACTTTTTAGACACTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATT
260 GTCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATT
* * * * *
1380656 AAATTCTAGACACTTTCAACATATCTGATAGTGTTTTAC
325 AAATTATCGACACTTTCAACATATCCGGTAGCGTTTTAC
* *
1380695 CGGTTTTGTCATTTTGAGACATGTTTTGTCATATTTTTACATGTTAACAATATATTGTTATGGAT
1 CGGTTTTGTCATTTTGAGACCTGTTTTGTCATATTTTTACCTG-T-----TATATTGTTAT-GAT
*
1380760 CGATACATTTTTTTAAAGTATCGACATTTTATAGGCGCTATAA---CTTCTCTTTTAAATTCCAA
59 CGATACATTTTTTTAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAA
*
1380822 AAGTGTCGATAATTATATTAAAGTATCGACACTTTCAACATATTCGGTAGTTATTTACCTGTTTT
124 AAGTGTCGATAATTATATTAAAGTATCGACACTTTCAACATATCCGGTAGTTATTTACCTGTTTT
1380887 GTCATTTTGAGACCAGTTTTGTCATATTTTTAGCTGTTATATTGTTATGGATCGATACATTTTCA
189 GTCATTTTGAGACCAGTTTTGTCATATTTTTAGCTGTTATATTGTTATGGATCGATACATTTTCA
* * ** * *
1380952 TAAAGTTTCAACTTTTTTTAGGCGTTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATTCT
254 TAAAGTGTCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACT
* *
1381017 TATATTAAATTATCGACACTTTCAACATATCTGGTAGCATTTTAC
319 TATATTAAATTATCGACACTTTCAACATATCCGGTAGCGTTTTAC
*
1381062 C-GTTTTGTTATTTTGAGACC
1 CGGTTTTGTCATTTTGAGACC
1381082 GGTTATATTG
Statistics
Matches: 1045, Mismatches: 59, Indels: 60
0.90 0.05 0.05
Matches are distributed among these distances:
363 111 0.11
364 269 0.26
365 2 0.00
366 17 0.02
367 243 0.23
370 56 0.05
371 1 0.00
372 1 0.00
375 1 0.00
377 1 0.00
382 1 0.00
383 92 0.09
384 250 0.24
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (363 bp):
CGGTTTTGTCATTTTGAGACCTGTTTTGTCATATTTTTACCTGTTATATTGTTATGATCGATACA
TTTTTTTAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTC
GATAATTATATTAAAGTATCGACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTT
TGAGACCAGTTTTGTCATATTTTTAGCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTG
TCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTA
AATTATCGACACTTTCAACATATCCGGTAGCGTTTTAC
Found at i:1380491 original size:566 final size:562
Alignment explanation
Indices: 1379398--1381081 Score: 2341
Period size: 566 Copynumber: 3.0 Consensus size: 562
1379388 ACTTTATGTT
* * *
1379398 GACCTATTTTCTCATATTTTTAGCTGTTATATTATTATCGATCGATACATTTTCATAAAGTGTCG
1 GACCTATTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCG
1379463 ACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAAT
66 ACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAAT
** * * *
1379528 TATCCTCACTTTCAACATATCCGGTAGCGT-TTTACCGGTTTTGTCATTTTAAGATCGGTTTTGT
131 TATCGACACTTTCAACATATCCGGTA--GTATTTA-CAGTTTTGTCATTTTTAGACCGGTTTTGT
* *
1379592 CATTTTGAGAACGATTTTGTCATATTTTTACCTGTTATATTA-TTATGGATCGATACATTTTTTT
193 CATTTTGAGACCGGTTTTGTCATATTTTTA-CTGTTATA-TAGTTATGGATCGATACA-TTTTTT
* *
1379656 TAAAGTATCGACACTTTATAGGTGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACT
255 TAAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACT
*
1379721 TATATTAAAGTATCGACACTTTCAACATATTCGGTAGTTATTTACCTGTTTTGTGATTTTGAGAC
320 TATATTAAAGTATCGACACTTTCAACATATTCGGTAGTTATTTACCTGTTTTGTCATTTTGAGAC
* *
1379786 CAGATTTGTCATATTTTTAGCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACA
385 CAGTTTTGTCATATTTTTAGCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTATCGACA
* *
1379851 CTTTTTAGGCGC-ATAACTTTTTCTCTTTTAAATTCTAAAAGTGTCGATACTTATATTAAATTAT
450 CTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAATTAT
*
1379915 CGACACTTTCAACATATCCGGTATCTTTTTACCGGTTTTGTCATTTTTA
515 CGACACTTTCAACATATCCGGTATCTTTTTACC-GTTTTGTCATTTTGA
* * * *
1379964 GACCTCTTTTGTCATATTTTTACCTGTTATATTGTTATAGATCGATACATTTT-TTAAAAGTATC
1 GACCTATTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCAT-AAAGTGTC
*
1380028 GACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTTCA-AAAGTGTCGATACTTATATTAA
65 GACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAA-TTCAGAAAGTGTCGATACTTATATTAA
* * *
1380092 AGTATCGACACTTTAAACATATCCGGTAGTTATTTACATGTTTTGTCATTTTTAGACCGATTTTG
129 ATTATCGACACTTTCAACATATCCGGTAG-TATTTACA-GTTTTGTCATTTTTAGACCGGTTTTG
**
1380157 TCATTTTGAGACCGGTTTTGTCATATTTTTAGCTGTTATATAGTTATGGATCGATACATTTTCAT
192 TCATTTTGAGACCGGTTTTGTCATATTTTTA-CTGTTATATAGTTATGGATCGATACATTTTTTT
*
1380222 AAAGTGTCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATT-CAGAAAGTGTCGATACT
256 AAAGTATCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCCA-AAAGTGTCGATACT
* * * * *
1380286 TATATTAAATTATCGACACTTTTAACATATCCGGTAGCGT-TTTACCGGTTTTGTCATTTTGAGA
320 TATATTAAAGTATCGACACTTTCAACATATTCGGTAG-TTATTTACCTGTTTTGTCATTTTGAGA
* * * **
1380350 CCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGAATCGATACATTTTTTTAAAGTATCGAC
384 CCAGTTTTGTCATATTTTTAGCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTATCGAC
* * *
1380415 ACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATAATTATATTAAAGTA
449 ACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAATTA
* *
1380480 TCGATACTTTCAACATATCCGGTAGT-TATTTACCTGTTTTGTCATTTTGA
514 TCGACACTTTCAACATATCCGGTA-TCTTTTTACC-GTTTTGTCATTTTGA
** * *
1380530 GACCGGTTTTGTCATATTTTTAGATGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCG
1 GACCTATTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCG
* *
1380595 ACACTTTTTAGACACTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAAT
66 ACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAAT
* *
1380660 TCTAGACACTTTCAACATAT-C--T-G-A--T--AG---TG----TTTT--ACCGGTTTTGTCAT
131 TATCGACACTTTCAACATATCCGGTAGTATTTACAGTTTTGTCATTTTTAGACCGGTTTTGTCAT
**
1380707 TTTGAGACATGTTTTGTCATATTTTTACATGTTAACAATATATTGTTATGGATCGATACATTTTT
196 TTTGAGACCGGTTTTGTCATATTTTTAC-TGTT----ATATA--GTTATGGATCGATACATTTTT
1380772 TTAAAGTATCGACA-TTTTATAGGCGCTATAA---CTTCTCTTTTAAATTCCAAAAGTGTCGATA
254 TTAAAGTATCGACACTTTT-TAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATA
*
1380833 ATTATATTAAAGTATCGACACTTTCAACATATTCGGTAGTTATTTACCTGTTTTGTCATTTTGAG
318 CTTATATTAAAGTATCGACACTTTCAACATATTCGGTAGTTATTTACCTGTTTTGTCATTTTGAG
* *
1380898 ACCAGTTTTGTCATATTTTTAGCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTTTCAA
383 ACCAGTTTTGTCATATTTTTAGCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTATCGA
** * *
1380963 CTTTTTTTAGGCGTTATAACTTCTTCTCTTTTAAATT-CAGAAAGTGTCGATTCTTATATTAAAT
448 CACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCCA-AAAGTGTCGATACTTATATTAAAT
* * * *
1381027 TATCGACACTTTCAACATATCTGGTAGCATTTTACCGTTTTGTTATTTTGA
512 TATCGACACTTTCAACATATCCGGTATCTTTTTACCGTTTTGTCATTTTGA
1381078 GACC
1 GACC
1381082 GGTTATATTG
Statistics
Matches: 1002, Mismatches: 92, Indels: 66
0.86 0.08 0.06
Matches are distributed among these distances:
545 1 0.00
546 42 0.04
548 25 0.02
549 226 0.23
550 7 0.01
551 4 0.00
552 46 0.05
555 1 0.00
556 1 0.00
558 1 0.00
560 1 0.00
562 1 0.00
563 1 0.00
564 3 0.00
565 199 0.20
566 437 0.44
567 6 0.01
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (562 bp):
GACCTATTTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCG
ACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAAT
TATCGACACTTTCAACATATCCGGTAGTATTTACAGTTTTGTCATTTTTAGACCGGTTTTGTCAT
TTTGAGACCGGTTTTGTCATATTTTTACTGTTATATAGTTATGGATCGATACATTTTTTTAAAGT
ATCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATT
AAAGTATCGACACTTTCAACATATTCGGTAGTTATTTACCTGTTTTGTCATTTTGAGACCAGTTT
TGTCATATTTTTAGCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTATCGACACTTTTT
AGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATATTAAATTATCGACAC
TTTCAACATATCCGGTATCTTTTTACCGTTTTGTCATTTTGA
Found at i:1389912 original size:30 final size:28
Alignment explanation
Indices: 1389818--1389914 Score: 72
Period size: 29 Copynumber: 3.2 Consensus size: 28
1389808 TTTATAAAGG
*
1389818 CTAAAATAGAGAAAAACAAAAACTTTAAGGAT
1 CTAAAATA-A-AAAAA-TAAAA-TTTAAGGAT
* * *
1389850 C-AAAATCAAAAAACATAAAGTTAAAGTA-
1 CTAAAAT-AAAAAA-ATAAAATTTAAGGAT
1389878 CTAAAATAACAAAAATACAAATTTAAGGAT
1 CTAAAATAA-AAAAATA-AAATTTAAGGAT
1389908 CTAAAAT
1 CTAAAAT
1389915 GATATTAACT
Statistics
Matches: 52, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
28 6 0.12
29 23 0.44
30 14 0.27
31 7 0.13
32 2 0.04
ACGTcount: A:0.61, C:0.10, G:0.08, T:0.21
Consensus pattern (28 bp):
CTAAAATAAAAAAATAAAATTTAAGGAT
Found at i:1390497 original size:24 final size:24
Alignment explanation
Indices: 1390470--1390525 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
1390460 TTCACTTAAA
1390470 TAACCTAAATCTTTAAACTAAAAT
1 TAACCTAAATCTTTAAACTAAAAT
1390494 TAACCTAAATCTTTAAACTAAAAT
1 TAACCTAAATCTTTAAACTAAAAT
1390518 TAACCTAA
1 TAACCTAA
1390526 TAACTAAAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (24 bp):
TAACCTAAATCTTTAAACTAAAAT
Found at i:1390509 original size:13 final size:13
Alignment explanation
Indices: 1390474--1390515 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
1390464 CTTAAATAAC
1390474 CTAAATCTTTAAA
1 CTAAATCTTTAAA
* *
1390487 CTAAA--ATTAAC
1 CTAAATCTTTAAA
1390498 CTAAATCTTTAAA
1 CTAAATCTTTAAA
1390511 CTAAA
1 CTAAA
1390516 ATTAACCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
11 9 0.39
13 14 0.61
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (13 bp):
CTAAATCTTTAAA
Found at i:1391870 original size:91 final size:91
Alignment explanation
Indices: 1391715--1391884 Score: 304
Period size: 91 Copynumber: 1.9 Consensus size: 91
1391705 AAGCATTGGA
*
1391715 TTGAACAAGTTCTTCTCATTATGAAATTCTTCTTCCTTGTTGGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAAATTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAAC
1391780 TCTTCATTGGAAATAATGATACAAGG
66 TCTTCATTGGAAATAATGATACAAGG
* * *
1391806 TTGAACAAGTTCTTTTCATTATGAACTTCTTCTTTCTCGTTGGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAAATTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAAC
1391871 TCTTCATTGGAAAT
66 TCTTCATTGGAAAT
1391885 GTCAATCCCT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 75 1.00
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.43
Consensus pattern (91 bp):
TTGAACAAGTTCTTCTCATTATGAAATTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAAC
TCTTCATTGGAAATAATGATACAAGG
Found at i:1392166 original size:228 final size:226
Alignment explanation
Indices: 1391718--1392347 Score: 904
Period size: 228 Copynumber: 2.8 Consensus size: 226
1391708 CATTGGATTG
* * *
1391718 AACAAGTTCTTCTCATTATGAAATTCTTCTTCCT-TGTTGGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTC
* ** * * * *
1391782 TTCATTGGAAATAATGATACAAGGTTGAACAAGTTCTTTTCATTATGAACTTCTTCTTTCTCGTT
66 TCCATTGGAAATGTTGATGCGAGATTGAACAAGTTCTTCTCATTATGAACTTCTTC-TTCTCGTT
** * * *
1391847 GGATGAGTTCTTCTCATTATGAACTCTTCATTGGAAATGTCAATCCCTCTAGCTAGGTGTCACTG
130 GGATGAGTTCTTCTCATTATGAACTCTTCATTGGAAATGTTGATCCCTCAAGCGAGGCGTCACTG
* *
1391912 ATTCGAAATGCCGTGAATCGAGTGATAGGTCA
195 ATTCGAAATGCCATGAATCAAGTGATAGGTCA
* * *
1391944 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGCCGGATGAGTTCTTCTCATTATGAACTA
1 AACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTC
* *
1392009 TCCATTGGAAATGTCTGATGTGAGATCGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTCGT
66 TCCATTGGAAATGT-TGATGCGAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCT-TCTCGT
* * * *
1392074 TGGATGAGTTCTTCTCATTATGAAATCTTCACTGAAAATGTTGATTCCTCAAGCGAGGCGTCACT
129 TGGATGAGTTCTTCTCATTATGAACTCTTCATTGGAAATGTTGATCCCTCAAGCGAGGCGTCACT
* *
1392139 GATTCGAAATGTCATGAATCAAGTGATAGGTCG
194 GATTCGAAATGCCATGAATCAAGTGATAGGTCA
* * * *
1392172 AACAAGTTCTTCTCATTATTAACTTCTTCTCCCTCTATCGGATGAGTTCTTATTATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTC
*
1392237 TCTATTGGAAATGTTGATGCGA-AGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGT
66 TCCATTGGAAATGTTGATGCGAGA-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTCGT
1392301 TGGATGAGTTCTTCTCATTATGAACTCTTCATTGGAAATGTTGATCC
129 TGGATGAGTTCTTCTCATTATGAACTCTTCATTGGAAATGTTGATCC
1392348 ATCTCTTTCT
Statistics
Matches: 357, Mismatches: 42, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
226 33 0.09
227 126 0.35
228 198 0.55
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (226 bp):
AACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTC
TCCATTGGAAATGTTGATGCGAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTCGTTG
GATGAGTTCTTCTCATTATGAACTCTTCATTGGAAATGTTGATCCCTCAAGCGAGGCGTCACTGA
TTCGAAATGCCATGAATCAAGTGATAGGTCA
Found at i:1392336 original size:91 final size:92
Alignment explanation
Indices: 1392171--1392345 Score: 275
Period size: 91 Copynumber: 1.9 Consensus size: 92
1392161 GTGATAGGTC
* *
1392171 GAACAAGTTCTTCTCATTATTAACTTCTTCTCCCTCTATCGGATGAGTTCTTATTATTATGAACT
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTATCATTATGAACT
1392236 CTCTATTGGAAATGTTGATGCGAAGTT
66 CTCTATTGGAAATGTTGATGCGAAGTT
* *
1392263 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGT-T-GGATGAGTTCTTCTCATTATGAAC
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTC-TATCGGATGAGTTCTTATCATTATGAAC
1392326 TCT-TCATTGGAAATGTTGAT
65 TCTCT-ATTGGAAATGTTGAT
1392346 CCATCTCTTT
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
90 1 0.01
91 40 0.52
92 35 0.45
93 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.42
Consensus pattern (92 bp):
GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTATCATTATGAACT
CTCTATTGGAAATGTTGATGCGAAGTT
Found at i:1392959 original size:76 final size:73
Alignment explanation
Indices: 1392857--1393036 Score: 209
Period size: 76 Copynumber: 2.4 Consensus size: 73
1392847 CGAGTGAGAT
* *
1392857 AAATTTTGTTTCGAAGGAAAATTGTCTCAAGCAAGACGAAGTAAGTTTTAAGAAAAACCATCTCA
1 AAATTTTGTTTC-AAGGGAAACTGTCTCAAGCAAGACGAAGTAAGTTTTAAGAAAAACCATCTCA
*
1392922 AGTGAGATTC-
65 AGGGAGA--CA
* * * ** * *
1392932 AATTTATTGTTTCAAGGGAAAGCTGTCTCAAGCGAGACGAATTTGGTTTTAAGAGAAACCATCTT
1 AAATT-TTGTTTCAAGGGAAA-CTGTCTCAAGCAAGACGAAGTAAGTTTTAAGAAAAACCATCTC
1392997 AAGGGAGACA
64 AAGGGAGACA
*
1393007 AAATTTTGTTTCAAGAGAAACTGTCTCAAG
1 AAATTTTGTTTCAAGGGAAACTGTCTCAAG
1393037 AGATACAAAT
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
73 10 0.11
74 15 0.17
75 15 0.17
76 50 0.56
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (73 bp):
AAATTTTGTTTCAAGGGAAACTGTCTCAAGCAAGACGAAGTAAGTTTTAAGAAAAACCATCTCAA
GGGAGACA
Found at i:1393120 original size:33 final size:33
Alignment explanation
Indices: 1393081--1393144 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
1393071 AAATTTTGTG
* * *
1393081 TTTCAAGAGAAATTTTCTCAAGGGAGACAAATT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAATT
*
1393114 TTTCAAGGGAAACTGTCTCAAGAGAGACAAA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAA
1393145 ATTTATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (33 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAATT
Found at i:1393144 original size:99 final size:99
Alignment explanation
Indices: 1392977--1393234 Score: 315
Period size: 99 Copynumber: 2.6 Consensus size: 99
1392967 GACGAATTTG
* * * * *
1392977 GTTTTAAGAGAAACCATCTTAAGGGAGACAAAATTTTGTTTCAAGAGAAACTGTCTCAAGAGATA
1 GTTTCAAGAGAAACTATCTCAAGGGAGAC-AAA-TTT-TTTCAAGGGAAACTGTCTCAAGAGAGA
* * * *
1393042 C-AAATTTTTTTTCAGGGGAAACGTTCTCAAAATTTTGT
63 CAAAATTTATTTT-AAGGGAAACGTTCTC-AAAGTTTAT
* *
1393080 GTTTCAAGAGAAATTTTCTCAAGGGAGACAAA-TTTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 GTTTCAAGAGAAACTATCTCAAGGGAGACAAATTTTTTCAAGGGAAACTGTCTCAAGAGAGACAA
* *
1393144 AATTTATTTTAAGGGAATCGTTTTCAAAGTTTAT
66 AATTTATTTTAAGGGAAACGTTCTCAAAGTTTAT
1393178 GTTTCAAGAGAAACTATCTCAAGGGAGACAAATTTTTTTCAAGGGAAAC-GTTCTCAA
1 GTTTCAAGAGAAACTATCTCAAGGGAGACAAA-TTTTTTCAAGGGAAACTG-TCTCAA
1393235 AATTTTGTGT
Statistics
Matches: 136, Mismatches: 15, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
98 37 0.27
99 39 0.29
100 33 0.24
102 3 0.02
103 24 0.18
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (99 bp):
GTTTCAAGAGAAACTATCTCAAGGGAGACAAATTTTTTCAAGGGAAACTGTCTCAAGAGAGACAA
AATTTATTTTAAGGGAAACGTTCTCAAAGTTTAT
Found at i:1393245 original size:163 final size:166
Alignment explanation
Indices: 1393005--1393304 Score: 482
Period size: 163 Copynumber: 1.8 Consensus size: 166
1392995 TTAAGGGAGA
* * *
1393005 CAAAATTTTGTTTCAAGAGAAACTGTCTCAAGAGATACAAATTTTTTTTCAGGGGAAACGTTCTC
1 CAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAATTTTTTTTCAAGGGAAACGTTCTC
* * * *
1393070 AAAATTTTGTGTTTCAAGAGAAATTTTCTCAAGGGAGAC-AAA-TT-TTTCAAGGGAAACTGTCT
66 AAAATTTTGTGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAATGTAT
1393132 CAAGAGAGACAAAATTTATTTTAAGGGAATCGTTTT
131 CAAGAGAGACAAAATTTATTTTAAGGGAATCGTTTT
* *
1393168 CAAAGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAA-TTTTTTTCAAGGGAAACGTTCT
1 CAAAATTT-TGTTTCAAGAGAAACTATCTCAAGAGAGACAAATTTTTTTTCAAGGGAAACGTTCT
1393232 CAAAATTTTGTGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAATGTA
65 CAAAATTTTGTGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAATGTA
1393297 TCAAGAGA
130 TCAAGAGA
1393305 TAAAATCTTC
Statistics
Matches: 124, Mismatches: 9, Indels: 5
0.90 0.07 0.04
Matches are distributed among these distances:
163 66 0.53
164 33 0.27
165 2 0.02
166 23 0.19
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (166 bp):
CAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAATTTTTTTTCAAGGGAAACGTTCTC
AAAATTTTGTGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAATGTAT
CAAGAGAGACAAAATTTATTTTAAGGGAATCGTTTT
Found at i:1393246 original size:65 final size:65
Alignment explanation
Indices: 1393114--1393291 Score: 252
Period size: 65 Copynumber: 2.7 Consensus size: 65
1393104 GAGACAAATT
* * * * *
1393114 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTT-AAGGGAATCGTTTTCAAAGTTTAT
1 TTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT-TTTTCAAGGGAAACGTTCTCAAAGTTTAT
1393178 G
65 G
* *
1393179 TTTCAAGAGAAACTATCTCAAGGGAGAC-AAATTTTTTTCAAGGGAAACGTTCTCAAAATTTTGT
1 TTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTTTTTCAAGGGAAACGTTCTC-AAAGTTTAT
1393243 G
65 G
*
1393244 TTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTCAAGGGAAA
1 TTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTTTTTCAAGGGAAA
1393292 ATGTATCAAG
Statistics
Matches: 102, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
63 4 0.04
64 19 0.19
65 61 0.60
66 18 0.18
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (65 bp):
TTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTTTTTCAAGGGAAACGTTCTCAAAGTTTATG
Found at i:1393391 original size:40 final size:40
Alignment explanation
Indices: 1393301--1393828 Score: 833
Period size: 40 Copynumber: 13.2 Consensus size: 40
1393291 AATGTATCAA
* * * ** *
1393301 GAGATAAAATCTTCTGTTTCGAGG-GAAACTATCTCAAGC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* * * *
1393340 GAGATAAAATCTTTTGTTTCAAAGAAAACCAATCTTGAGC
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
1393380 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGTGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
1393420 GAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
1393460 GAAATAAAATCTTCTGTTTCAAGGAAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGG-AAAAACAATCTTGAGT
1393501 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
1393541 GAGATAAAATCTTATGTTTCAAGGAAAAATAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1393581 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
1393621 GAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* *
1393661 GAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1393701 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
* * *
1393741 GAGATAAAATCTTTTGTTTCAAGGAAAAAAAATCTTGAAT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
*
1393781 GAAATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1393821 GAGATAAA
1 GAGATAAA
1393829 TCCTTTGTAT
Statistics
Matches: 451, Mismatches: 36, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
39 21 0.05
40 392 0.87
41 38 0.08
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.31
Consensus pattern (40 bp):
GAGATAAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
Found at i:1393654 original size:23 final size:23
Alignment explanation
Indices: 1393628--1393696 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 23
1393618 AGTGAGATAA
1393628 AATCTTTTGTTTCAAGGAAAAAC
1 AATCTTTTGTTTCAAGGAAAAAC
** * *
1393651 AATC--TTGAGT-GA-G-ATAA-
1 AATCTTTTGTTTCAAGGAAAAAC
1393668 AATCTTTTGTTTCAAGGAAAAAC
1 AATCTTTTGTTTCAAGGAAAAAC
1393691 AATCTT
1 AATCTT
1393697 GAATGAGATA
Statistics
Matches: 32, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
17 4 0.12
18 3 0.09
19 5 0.16
20 2 0.06
21 5 0.16
22 3 0.09
23 10 0.31
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (23 bp):
AATCTTTTGTTTCAAGGAAAAAC
Found at i:1393773 original size:23 final size:23
Alignment explanation
Indices: 1393746--1393816 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 23
1393736 TGAGTGAGAT
1393746 AAAATCTTTTGTTTCAAGGAAAA
1 AAAATCTTTTGTTTCAAGGAAAA
* *
1393769 AAAATC--TTG----AATGAAAT
1 AAAATCTTTTGTTTCAAGGAAAA
*
1393786 AAAATCTTCTGTTTCAAGGAAAA
1 AAAATCTTTTGTTTCAAGGAAAA
*
1393809 ACAATCTT
1 AAAATCTT
1393817 GAGTGAGATA
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
17 12 0.33
19 2 0.06
21 3 0.08
23 19 0.53
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.32
Consensus pattern (23 bp):
AAAATCTTTTGTTTCAAGGAAAA
Found at i:1394810 original size:54 final size:54
Alignment explanation
Indices: 1394721--1394834 Score: 165
Period size: 54 Copynumber: 2.1 Consensus size: 54
1394711 TAAACACTGG
* * * * *
1394721 TTTGTAAAACATTTGACAACACATTTATCATTTCCTGTGGTTTTTGCCCAGATT
1 TTTGTAAAACATTTGACAACACATTCATCACTTCCTGTGGCTTCTGCCCAAATT
*
1394775 TTTGTAAAACATTTGACAACACATTCATCCCTTCCTGTGGCTTCTGCCCAAATT
1 TTTGTAAAACATTTGACAACACATTCATCACTTCCTGTGGCTTCTGCCCAAATT
1394829 TCTTGT
1 T-TTGT
1394835 CAGTGAAGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
54 49 0.92
55 4 0.08
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (54 bp):
TTTGTAAAACATTTGACAACACATTCATCACTTCCTGTGGCTTCTGCCCAAATT
Found at i:1396350 original size:17 final size:19
Alignment explanation
Indices: 1396309--1396351 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
1396299 TTGTACCCTT
**
1396309 AGTGCATCGGTGCACTAAG
1 AGTGCATCAATGCACTAAG
1396328 AGTGCATCAATGCA-TAA-
1 AGTGCATCAATGCACTAAG
1396345 AGTGCAT
1 AGTGCAT
1396352 TCGATGTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 3 0.14
19 12 0.55
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (19 bp):
AGTGCATCAATGCACTAAG
Found at i:1396462 original size:65 final size:64
Alignment explanation
Indices: 1396329--1396488 Score: 191
Period size: 65 Copynumber: 2.5 Consensus size: 64
1396319 TGCACTAAGA
* * *
1396329 GTGCATCAATGCATAAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGAA-TGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
* * *
1396393 GTGCATCGATGCATCGAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-T
1 GTGCATCGATGCAT-GAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGCT
*
1396456 AT
64 -G
1396458 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATG-AATGCATTCGATGTT
1396489 CAATTTAATT
Statistics
Matches: 84, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
64 26 0.31
65 55 0.65
66 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATGAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
Found at i:1396527 original size:65 final size:63
Alignment explanation
Indices: 1396329--1396537 Score: 189
Period size: 65 Copynumber: 3.2 Consensus size: 63
1396319 TGCACTAAGA
* * * *
1396329 GTGCATCAATGCAT-AAAGTGCATTCGATGTTTCA-AAATAGC-CAGAGTGCATCGATGCATGGC
1 GTGCATCGATGCATCGAA-TGCATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGGT
1396391 TG
62 TG
*
1396393 GTGCATCGATGCATCGAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCGAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGT-T
1396458 -
63 G
**
1396458 GTGCATCGATGCAT-GAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGA
1 GTGCATCGATGCATCG-AATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-
1396520 TTG
61 TTG
*
1396523 GTGCATCGGTGCATC
1 GTGCATCGATGCATC
1396538 ACTCTGAAAA
Statistics
Matches: 123, Mismatches: 9, Indels: 24
0.79 0.06 0.15
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 46 0.37
65 65 0.53
66 5 0.04
67 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATCGAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTG
Found at i:1396934 original size:21 final size:25
Alignment explanation
Indices: 1396873--1396922 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1396863 CTCCCCCTTA
1396873 CTATAACACTTCTCCCTTAAAACAT
1 CTATAACACTTCTCCCTTAAAACAT
1396898 CTATAACACTTCTCCCTTAAAACAT
1 CTATAACACTTCTCCCTTAAAACAT
1396923 AACATTTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (25 bp):
CTATAACACTTCTCCCTTAAAACAT
Found at i:1411496 original size:30 final size:28
Alignment explanation
Indices: 1411402--1411498 Score: 72
Period size: 29 Copynumber: 3.2 Consensus size: 28
1411392 TTTATAAAGG
*
1411402 CTAAAATAGAGAAAAACAAAAACTTTAAGGAT
1 CTAAAATA-A-AAAAA-TAAAA-TTTAAGGAT
* * *
1411434 C-AAAATCAAAAAACATAAAGTTAAAGTA-
1 CTAAAAT-AAAAAA-ATAAAATTTAAGGAT
1411462 CTAAAATAACAAAAATACAAATTTAAGGAT
1 CTAAAATAA-AAAAATA-AAATTTAAGGAT
1411492 CTAAAAT
1 CTAAAAT
1411499 GATATTATCT
Statistics
Matches: 52, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
28 6 0.12
29 23 0.44
30 14 0.27
31 7 0.13
32 2 0.04
ACGTcount: A:0.61, C:0.10, G:0.08, T:0.21
Consensus pattern (28 bp):
CTAAAATAAAAAAATAAAATTTAAGGAT
Found at i:1418852 original size:64 final size:64
Alignment explanation
Indices: 1418767--1418911 Score: 182
Period size: 64 Copynumber: 2.3 Consensus size: 64
1418757 GATGCACTAT
* * * * *
1418767 TGTGTATTATCTGAATATGACATTAACACATATATGCATTATCTGAATGCGACACTGACAATAA
1 TGTGCATTATCTGAATGTGACACTAACACATATATGCAGTATCTGAATGCGACACTAACAATAA
* * * * * **
1418831 TGTGCATTATCTTAATGTGACACTAACACTTCTGTGCAGTATCTGAATGCGACACTAACACTCT
1 TGTGCATTATCTGAATGTGACACTAACACATATATGCAGTATCTGAATGCGACACTAACAATAA
1418895 TGTGCATTATCTGAATG
1 TGTGCATTATCTGAATG
1418912 GAACACTCTG
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
64 68 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.34
Consensus pattern (64 bp):
TGTGCATTATCTGAATGTGACACTAACACATATATGCAGTATCTGAATGCGACACTAACAATAA
Found at i:1418918 original size:32 final size:31
Alignment explanation
Indices: 1418761--1418911 Score: 149
Period size: 32 Copynumber: 4.7 Consensus size: 31
1418751 ACACGTGATG
* ** *
1418761 CACTATTGTGTATTATCTGAATATGACATTAA
1 CACT-TTGTGCATTATCTGAATGCGACACTAA
* * *
1418793 CACATATATGCATTATCTGAATGCGACACTGA
1 CAC-TTTGTGCATTATCTGAATGCGACACTAA
* * * *
1418825 CAATAATGTGCATTATCTTAATGTGACACTAA
1 CACT-TTGTGCATTATCTGAATGCGACACTAA
*
1418857 CACTTCTGTGCAGTATCTGAATGCGACACTAA
1 CACTT-TGTGCATTATCTGAATGCGACACTAA
1418889 CACTCTTGTGCATTATCTGAATG
1 CACT-TTGTGCATTATCTGAATG
1418912 GAACACTCTG
Statistics
Matches: 97, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
31 1 0.01
32 94 0.97
33 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (31 bp):
CACTTTGTGCATTATCTGAATGCGACACTAA
Found at i:1419249 original size:16 final size:17
Alignment explanation
Indices: 1419230--1419277 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
1419220 GCAACTAAGT
1419230 TAGCT-ACACACTAGAA
1 TAGCTGACACACTAGAA
1419246 TAGCTTGACACACTAGAA
1 TAGC-TGACACACTAGAA
1419264 TAGCTCGACACACT
1 TAGCT-GACACACT
1419278 TAAGTGAGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.14
17 2 0.07
18 23 0.79
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.21
Consensus pattern (17 bp):
TAGCTGACACACTAGAA
Found at i:1419276 original size:20 final size:18
Alignment explanation
Indices: 1419235--1419277 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
1419225 TAAGTTAGCT
*
1419235 ACACACTAGAATAGCTTG
1 ACACACTAGAATAGCTCG
1419253 ACACACTAGAATAGCTCG
1 ACACACTAGAATAGCTCG
1419271 ACACACT
1 ACACACT
1419278 TAAGTGAGGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.40, C:0.28, G:0.14, T:0.19
Consensus pattern (18 bp):
ACACACTAGAATAGCTCG
Found at i:1421878 original size:30 final size:29
Alignment explanation
Indices: 1421829--1421894 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
1421819 TAAAGTTTAG
* * * *
1421829 AAAAATTTAGGGACTAAAAGGGTAATTTTC
1 AAAAGTTTAAGGACCAAAAGGGTAA-TTAC
*
1421859 AAAAGTTTAAGGACCAAAAGTGTAATTAC
1 AAAAGTTTAAGGACCAAAAGGGTAATTAC
1421888 AAAAGTT
1 AAAAGTT
1421895 ATGTATTTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 10 0.32
30 21 0.68
ACGTcount: A:0.47, C:0.08, G:0.18, T:0.27
Consensus pattern (29 bp):
AAAAGTTTAAGGACCAAAAGGGTAATTAC
Found at i:1424565 original size:34 final size:34
Alignment explanation
Indices: 1424520--1424604 Score: 107
Period size: 34 Copynumber: 2.5 Consensus size: 34
1424510 ATAATTGGTA
* *
1424520 GTACTATAGTGTCTAGCAAAGGAACATAGTAAAT
1 GTACTAAAGTGTCTAGCAAAGGAACATAGTAAAG
* * * *
1424554 GTACTAGAGTGTCTAGCAAAGGCATATAGTATAG
1 GTACTAAAGTGTCTAGCAAAGGAACATAGTAAAG
*
1424588 GTATTAAAGTGTCTAGC
1 GTACTAAAGTGTCTAGC
1424605 GAAGACACGT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (34 bp):
GTACTAAAGTGTCTAGCAAAGGAACATAGTAAAG
Found at i:1431101 original size:2 final size:2
Alignment explanation
Indices: 1431094--1431124 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1431084 GATAGTTATT
1431094 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1431125 CCTATAGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1431105 original size:23 final size:23
Alignment explanation
Indices: 1431060--1431105 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1431050 TTATACCTAT
*
1431060 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATATTATA
*
1431083 AGATAGTTATTT-ATATATATATA
1 AGATACTTATTTCATATAT-TATA
1431106 TATATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATATTATA
Found at i:1432757 original size:17 final size:18
Alignment explanation
Indices: 1432708--1432771 Score: 62
Period size: 17 Copynumber: 3.6 Consensus size: 18
1432698 AATTGGAGTG
* **
1432708 CAAAAAGAACGAAAAAGA
1 CAAAAAGAAAGAAAAATT
1432726 C-AAAAGAAGAGAAAAA-T
1 CAAAAAGAA-AGAAAAATT
1432743 CAGAAAAGAAA-AAAAATT
1 CA-AAAAGAAAGAAAAATT
1432761 CAAAAAGAAAG
1 CAAAAAGAAAG
1432772 CAAGCCAAGG
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 21 0.54
18 11 0.28
19 7 0.18
ACGTcount: A:0.72, C:0.08, G:0.16, T:0.05
Consensus pattern (18 bp):
CAAAAAGAAAGAAAAATT
Found at i:1435682 original size:23 final size:23
Alignment explanation
Indices: 1435637--1435682 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1435627 TTATACCTAT
*
1435637 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
1435660 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
1435683 TATTATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:1444237 original size:3 final size:3
Alignment explanation
Indices: 1444229--1444257 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1444219 TAAAAGAAAT
1444229 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1444258 GGTCTTCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1444657 original size:130 final size:130
Alignment explanation
Indices: 1444419--1444657 Score: 327
Period size: 130 Copynumber: 1.8 Consensus size: 130
1444409 TTGAAATCTG
* * *
1444419 AAAAGGGATATGCTCCACTGCTTTTCAGGGTAGATCAGATTCGAAAATGTTGATTTACTCCACTG
1 AAAAGGGATATGCTCCACTGCTCTTCAGGGTAGATCAGATTCGAAAATATTGATTCACTCCACTG
* * * * * *
1444484 CTCTTCAGGGTAGATTGAATCGAGGCAGATTTGTTCCATTGCTCCTCAGGGAAGATCAAATCAGA
66 CTCTTCAGGGAAGATTAAATCAAGGCAAATTTGATCCACTGCTCCTCAGGGAAGATCAAATCAGA
*** * *
1444549 AAAAGGGATATGCTCTGTTGCTCTTCAGGGTAGATCATATAT-GAAAATATTGATTCATTCCACT
1 AAAAGGGATATGCTCCACTGCTCTTCAGGGTAGATCAGAT-TCGAAAATATTGATTCACTCCACT
*
1444613 GCTCTTCAGGGAAGATTAAATCAAGGTAAATTTGATCCACTGCTC
65 GCTCTTCAGGGAAGATTAAATCAAGGCAAATTTGATCCACTGCTC
1444658 TTCATAGAAG
Statistics
Matches: 93, Mismatches: 15, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
130 92 0.99
131 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (130 bp):
AAAAGGGATATGCTCCACTGCTCTTCAGGGTAGATCAGATTCGAAAATATTGATTCACTCCACTG
CTCTTCAGGGAAGATTAAATCAAGGCAAATTTGATCCACTGCTCCTCAGGGAAGATCAAATCAGA
Found at i:1444659 original size:41 final size:41
Alignment explanation
Indices: 1444607--1444716 Score: 166
Period size: 41 Copynumber: 2.7 Consensus size: 41
1444597 ATTGATTCAT
*
1444607 TCCACTGCTCTTCAGGGAAGATTAAATCAAGGTAAATTTGA
1 TCCACTGCTCTTCATGGAAGATTAAATCAAGGTAAATTTGA
* * * *
1444648 TCCACTGCTCTTCATAGAAGATTGAATCAAGGTAGATTTGT
1 TCCACTGCTCTTCATGGAAGATTAAATCAAGGTAAATTTGA
*
1444689 TCCACTGCTCTTCATGGAAGATCAAATC
1 TCCACTGCTCTTCATGGAAGATTAAATC
1444717 TGAAACAAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 61 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (41 bp):
TCCACTGCTCTTCATGGAAGATTAAATCAAGGTAAATTTGA
Found at i:1444794 original size:45 final size:45
Alignment explanation
Indices: 1444682--1444801 Score: 116
Period size: 46 Copynumber: 2.6 Consensus size: 45
1444672 AATCAAGGTA
*
1444682 GATTTGTTCCACTGCTCTTCATGGAAGATCAAATCTGAAACAAAAG
1 GATTTGTTCCACTGCTCTTCAGGGAAGATCAAATCTGAAAC-AAAG
* ** * * * * **
1444728 GATCTCCTCTACTGCTTTTCAGGGGAGATCAGATCTGGAAAC-ATT
1 GATTTGTTCCACTGCTCTTCAGGGAAGATCAAATCT-GAAACAAAG
*
1444773 GATTTGTTCCACTGCTCTTCAGGAAAGAT
1 GATTTGTTCCACTGCTCTTCAGGGAAGAT
1444802 TGAATCAAGA
Statistics
Matches: 56, Mismatches: 17, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
45 23 0.41
46 28 0.50
47 5 0.09
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (45 bp):
GATTTGTTCCACTGCTCTTCAGGGAAGATCAAATCTGAAACAAAG
Found at i:1444802 original size:132 final size:132
Alignment explanation
Indices: 1444642--1444939 Score: 332
Period size: 132 Copynumber: 2.3 Consensus size: 132
1444632 ATCAAGGTAA
* * * *
1444642 ATTTGATCCACTGCTCTTCA-TAGAAGATTGAATCAAGGTAGATTTGTTCCACT-GCTCTTCATG
1 ATTTGTTCCACTGCTCTTCAGGA-AAGATTGAATCAAGATAGATTTGTTCCA-TGGCTCTTCAGG
* * * * **
1444705 GAAGATCAAATCTGAAACAAAAGGATCT-CCTCTACTGCTTTTCAGGGGAGATCAGATCTGGAAA
64 GAAGATCAAATCTAAAAAAAAAGGATCTACTTC-ACTGCTCTTCAGGGGAGATCAGATCCAGAAA
1444769 CATTG
128 CATTG
** *
1444774 ATTTGTTCCACTGCTCTTCAGGAAAGATTGAATCAAGATAGATTTGTTTTATGGCTCTTTAGGGA
1 ATTTGTTCCACTGCTCTTCAGGAAAGATTGAATCAAGATAGATTTGTTCCATGGCTCTTCAGGGA
* * * * * **
1444839 AGTTCAAATCTAAAAAAAAAGGCTCTACTTCACTGGTCTTCAGGGTAGATTAGATCCAGAAATGT
66 AGATCAAATCTAAAAAAAAAGGATCTACTTCACTGCTCTTCAGGGGAGATCAGATCCAGAAACAT
1444904 TG
131 TG
** * *
1444906 ATTCATTTCACTGCTCTTCAGGGAAGATTGAATC
1 ATTTGTTCCACTGCTCTTCAGGAAAGATTGAATC
1444940 GGGTTTGATT
Statistics
Matches: 139, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
131 1 0.01
132 134 0.96
133 4 0.03
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (132 bp):
ATTTGTTCCACTGCTCTTCAGGAAAGATTGAATCAAGATAGATTTGTTCCATGGCTCTTCAGGGA
AGATCAAATCTAAAAAAAAAGGATCTACTTCACTGCTCTTCAGGGGAGATCAGATCCAGAAACAT
TG
Found at i:1446131 original size:6 final size:6
Alignment explanation
Indices: 1446120--1446199 Score: 53
Period size: 6 Copynumber: 13.5 Consensus size: 6
1446110 CCCCCTTTTA
* *
1446120 TTTATT TTTA-T TAT-TT TTTATT TTTATT TTTATTTT TTTCATT TTCATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTA--TT TTT-ATT TTTATT
* *
1446169 TTCATT TTCA-T TTTA-- TTTATT TCTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT T-TTATT TTT
1446200 TTCATTCTTA
Statistics
Matches: 62, Mismatches: 4, Indels: 16
0.76 0.05 0.20
Matches are distributed among these distances:
4 4 0.06
5 10 0.16
6 32 0.52
7 10 0.16
8 5 0.08
9 1 0.02
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:1446157 original size:13 final size:13
Alignment explanation
Indices: 1446115--1446156 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
1446105 TTGAACCCCC
1446115 TTTTATTTATTT-T
1 TTTTATTT-TTTAT
*
1446128 TATTATTTTTTAT
1 TTTTATTTTTTAT
1446141 TTTTA-TTTTTAT
1 TTTTATTTTTTAT
1446153 TTTT
1 TTTT
1446157 TTCATTTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 14 0.54
13 12 0.46
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTATTTTTTAT
Found at i:1446217 original size:17 final size:15
Alignment explanation
Indices: 1446140--1446225 Score: 51
Period size: 15 Copynumber: 5.8 Consensus size: 15
1446130 TTATTTTTTA
*
1446140 TTTTT-ATTTTTATT
1 TTTTTCATTCTTATT
1446154 TTTTTCATT-TTCA--
1 TTTTTCATTCTT-ATT
1446167 -TTTTCATT-TTCATT
1 TTTTTCATTCTT-ATT
1446181 TTATTT-ATTTCTTATT
1 TT-TTTCA-TTCTTATT
1446197 TTTTTCATTCTTATT
1 TTTTTCATTCTTATT
*
1446212 CCTTTTTCTTTCTT
1 --TTTTTCATTCTT
1446226 CAGACGAAGT
Statistics
Matches: 60, Mismatches: 1, Indels: 19
0.75 0.01 0.24
Matches are distributed among these distances:
12 12 0.20
14 7 0.12
15 17 0.28
16 11 0.18
17 13 0.22
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTCATTCTTATT
Found at i:1452817 original size:21 final size:22
Alignment explanation
Indices: 1452786--1452826 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1452776 CATAGCTATG
1452786 ATTTCATCTTCCAATTGTTTTC
1 ATTTCATCTTCCAATTGTTTTC
* *
1452808 ATTTC-TCTTCTAGTTGTTT
1 ATTTCATCTTCCAATTGTTT
1452827 ATTATGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.15, C:0.20, G:0.07, T:0.59
Consensus pattern (22 bp):
ATTTCATCTTCCAATTGTTTTC
Found at i:1456038 original size:22 final size:22
Alignment explanation
Indices: 1455998--1456039 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1455988 GGGATTCTTA
*
1455998 AGGTTTGGGTTGGGCTTTACCT
1 AGGTTTGGGTTAGGCTTTACCT
1456020 AGGTTTGGGTCTAGG-TTTAC
1 AGGTTTGGGT-TAGGCTTTAC
1456040 TATATGTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.12, C:0.12, G:0.36, T:0.40
Consensus pattern (22 bp):
AGGTTTGGGTTAGGCTTTACCT
Found at i:1458687 original size:20 final size:20
Alignment explanation
Indices: 1458662--1458712 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1458652 TTGGGTAAGG
1458662 GTATCGATACTGGAAGAACA
1 GTATCGATACTGGAAGAACA
1458682 GTATCGATACTGGAAGAACA
1 GTATCGATACTGGAAGAACA
*
1458702 GTACCGATACT
1 GTATCGATACT
1458713 ATAAAGTTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.22
Consensus pattern (20 bp):
GTATCGATACTGGAAGAACA
Found at i:1459654 original size:25 final size:23
Alignment explanation
Indices: 1459626--1459717 Score: 103
Period size: 23 Copynumber: 3.8 Consensus size: 23
1459616 GTTCTACGCT
*
1459626 GTCCTTCGGGACAAATTTCTATGTG
1 GTCCTTCAGGA-AAA-TTCTATGTG
**
1459651 GTCCTTCAGGAAAAAACTATGTG
1 GTCCTTCAGGAAAATTCTATGTG
**
1459674 GTCCTTTGGGAAAATTCTATGTG
1 GTCCTTCAGGAAAATTCTATGTG
1459697 GTCCTTCAGGACAATATTCTA
1 GTCCTTCAGGA-AA-ATTCTA
1459718 CACGGTTCTT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
23 35 0.62
24 5 0.09
25 16 0.29
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (23 bp):
GTCCTTCAGGAAAATTCTATGTG
Found at i:1459878 original size:19 final size:20
Alignment explanation
Indices: 1459846--1459884 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1459836 ATGGGCTAAA
*
1459846 TAAACTAATAGATAT-GAAT
1 TAAACAAATAGATATAGAAT
*
1459865 TAAACAAATTGATATAGAAT
1 TAAACAAATAGATATAGAAT
1459885 GAAAAGTGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.54, C:0.05, G:0.10, T:0.31
Consensus pattern (20 bp):
TAAACAAATAGATATAGAAT
Found at i:1461217 original size:23 final size:22
Alignment explanation
Indices: 1461191--1461234 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1461181 CCTCCAGGGT
* *
1461191 AAAGCTCTCTCCTTTTTTTCCTG
1 AAAGATCTCT-CTTTTTCTCCTG
*
1461214 AAAGATTTCTCTTTTTCTCCT
1 AAAGATCTCTCTTTTTCTCCT
1461235 TTTTCCGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.16, C:0.27, G:0.07, T:0.50
Consensus pattern (22 bp):
AAAGATCTCTCTTTTTCTCCTG
Found at i:1461769 original size:6 final size:6
Alignment explanation
Indices: 1461747--1461788 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
1461737 TTTGGGCATG
1461747 TAAA-A TAAATA -AAATA TAAATATA TAAATA TAAATA TAAATA
1 TAAATA TAAATA TAAATA T-AA-ATA TAAATA TAAATA TAAATA
1461789 ATAATAACGG
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
5 9 0.27
6 16 0.48
7 4 0.12
8 4 0.12
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
TAAATA
Found at i:1461775 original size:19 final size:19
Alignment explanation
Indices: 1461750--1461792 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1461740 GGGCATGTAA
1461750 AATAAATA-AAATATAAAT
1 AATAAATATAAATATAAAT
1461768 ATATAAATATAAATATAAAT
1 A-ATAAATATAAATATAAAT
1461788 AATAA
1 AATAA
1461793 TAACGGTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 1 0.04
19 11 0.48
20 11 0.48
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AATAAATATAAATATAAAT
Found at i:1461777 original size:14 final size:14
Alignment explanation
Indices: 1461758--1461784 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1461748 AAAATAAATA
1461758 AAATATAAATATAT
1 AAATATAAATATAT
1461772 AAATATAAATATA
1 AAATATAAATATA
1461785 AATAATAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATATAAATATAT
Found at i:1461795 original size:16 final size:16
Alignment explanation
Indices: 1461747--1461795 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 16
1461737 TTTGGGCATG
*
1461747 TAAA-ATAAATAAAATA
1 TAAATATAAATAATA-A
*
1461763 TAAATATATA-AAT-A
1 TAAATATAAATAATAA
1461777 TAAATATAAATAATAA
1 TAAATATAAATAATAA
1461793 TAA
1 TAA
1461796 CGGTCTCCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
14 10 0.37
15 3 0.11
16 10 0.37
17 4 0.15
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
TAAATATAAATAATAA
Found at i:1462137 original size:12 final size:12
Alignment explanation
Indices: 1462120--1462145 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1462110 AGAATTTACA
1462120 TATATCAAAATT
1 TATATCAAAATT
1462132 TATATCAAAATT
1 TATATCAAAATT
1462144 TA
1 TA
1462146 CGTGCATCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
TATATCAAAATT
Found at i:1463836 original size:20 final size:20
Alignment explanation
Indices: 1463787--1463841 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 20
1463777 TACATTAAGC
*
1463787 GGGTATCGATACCTTAATAG
1 GGGTATCGATACCATAATAG
1463807 GGTAGTATCGATACCATAGA-AG
1 GG--GTATCGATACCATA-ATAG
1463829 GGGTATCGATACC
1 GGGTATCGATACC
1463842 GAAGGACCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 13 0.42
22 17 0.55
23 1 0.03
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.25
Consensus pattern (20 bp):
GGGTATCGATACCATAATAG
Found at i:1464293 original size:81 final size:81
Alignment explanation
Indices: 1464158--1464358 Score: 323
Period size: 81 Copynumber: 2.5 Consensus size: 81
1464148 GTGATTACCA
* * *
1464158 AATGGCCTAACTGTGCAATTGGCAGAAAGATGTCAATTATGCCAGTTAGATGAACGGCTAAGTAC
1 AATGGCCTAACTGTGCAATTGGCAGAAAGGTGTCAATTATGCCACTTAGATGAACGACTAAGTAC
1464223 CGTTGAGTAAAAGAAT
66 CGTTGAGTAAAAGAAT
* *
1464239 AATGGCCTAACTGTGCAATTGGCATAAAGGTGTCAATTATGCCACTTAGATGAACGATTAAGTAC
1 AATGGCCTAACTGTGCAATTGGCAGAAAGGTGTCAATTATGCCACTTAGATGAACGACTAAGTAC
*
1464304 TGTTGAGTAAAAGAAT
66 CGTTGAGTAAAAGAAT
**
1464320 AATGTACTAACTGTGC-ATTGGCAGAAAGGTGTCAATTAT
1 AATGGCCTAACTGTGCAATTGGCAGAAAGGTGTCAATTAT
1464359 ACCGGTTAGA
Statistics
Matches: 111, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
80 22 0.20
81 89 0.80
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.27
Consensus pattern (81 bp):
AATGGCCTAACTGTGCAATTGGCAGAAAGGTGTCAATTATGCCACTTAGATGAACGACTAAGTAC
CGTTGAGTAAAAGAAT
Found at i:1468932 original size:81 final size:81
Alignment explanation
Indices: 1468817--1469199 Score: 599
Period size: 81 Copynumber: 4.8 Consensus size: 81
1468807 GTGATTACCA
* * * * *
1468817 AATGGCCTAACTATGTAATTGGCATAAAGGTGTCAATTATGCCAATTAGATGAACGGTTAAGTAT
1 AATGGCCTAACTGTGCAATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTAC
1468882 CGTTGAGTAAAAGAAT
66 CGTTGAGTAAAAGAAT
**
1468898 AATGGCCTAACTGTGCAATTCACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTAC
1 AATGGCCTAACTGTGCAATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTAC
1468963 CGTTGAGTAAAAGAAT
66 CGTTGAGTAAAAGAAT
* *
1468979 AATGGTCTAACAGTGCAATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTAC
1 AATGGCCTAACTGTGCAATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTAC
1469044 CGTTGAGTAAAAGAAT
66 CGTTGAGTAAAAGAAT
* * * *
1469060 AATGGCCTAACTGTGCAATTGGCAGAAAGGTGACAATTATGACATTTAGATGAACGGTTAAGTAT
1 AATGGCCTAACTGTGCAATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTAC
1469125 CGTTGAGTAAAAGAAT
66 CGTTGAGTAAAAGAAT
* ** *
1469141 AATGGCCTAACTTTGC-ATTGGCAGAAAGGTGTCAATTATATCAGTTAGACGAAC-GTTAA
1 AATGGCCTAACTGTGCAATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAA
1469200 ACAGTGTTGA
Statistics
Matches: 279, Mismatches: 23, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
79 5 0.02
80 33 0.12
81 241 0.86
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (81 bp):
AATGGCCTAACTGTGCAATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTAC
CGTTGAGTAAAAGAAT
Found at i:1476901 original size:7 final size:7
Alignment explanation
Indices: 1476891--1476948 Score: 116
Period size: 7 Copynumber: 8.3 Consensus size: 7
1476881 CCTGTAGGCT
1476891 GCATGAA
1 GCATGAA
1476898 GCATGAA
1 GCATGAA
1476905 GCATGAA
1 GCATGAA
1476912 GCATGAA
1 GCATGAA
1476919 GCATGAA
1 GCATGAA
1476926 GCATGAA
1 GCATGAA
1476933 GCATGAA
1 GCATGAA
1476940 GCATGAA
1 GCATGAA
1476947 GC
1 GC
1476949 TGGGTCTATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 51 1.00
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (7 bp):
GCATGAA
Found at i:1477279 original size:68 final size:68
Alignment explanation
Indices: 1477170--1477357 Score: 358
Period size: 68 Copynumber: 2.8 Consensus size: 68
1477160 CAGACATGAG
1477170 AGTTGTGGAAAAGAGCTTTAAATAGGAATGCTCGTTTTAGGAATTGAGCTTTCAGGGAAACACTA
1 AGTTGTGGAAAAGAGCTTTAAATAGGAATGCTCGTTTTAGGAATTGAGCTTTCAGGGAAACACTA
1477235 ATT
66 ATT
*
1477238 AGTTGTGGAAAAGAGCTTTAAATAGGAATGCTCGTTTTAGGAATTGAGCTTTCAGGGAAAGACTA
1 AGTTGTGGAAAAGAGCTTTAAATAGGAATGCTCGTTTTAGGAATTGAGCTTTCAGGGAAACACTA
1477303 ATT
66 ATT
*
1477306 AGTTGTGGAAAAGAGCTTTAAATAGGAATGTTCGTTTTAGGAATTGAGCTTT
1 AGTTGTGGAAAAGAGCTTTAAATAGGAATGCTCGTTTTAGGAATTGAGCTTT
1477358 GAGCGGCGTT
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 118 1.00
ACGTcount: A:0.33, C:0.09, G:0.26, T:0.32
Consensus pattern (68 bp):
AGTTGTGGAAAAGAGCTTTAAATAGGAATGCTCGTTTTAGGAATTGAGCTTTCAGGGAAACACTA
ATT
Found at i:1478646 original size:14 final size:14
Alignment explanation
Indices: 1478611--1478649 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1478601 TATTAAATTT
1478611 TAAAAAAAATGTTA
1 TAAAAAAAATGTTA
*
1478625 TATAAAAAATGTTA
1 TAAAAAAAATGTTA
*
1478639 AAAGAAAAAAT
1 TAA-AAAAAAT
1478650 AAAATAAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.26
Consensus pattern (14 bp):
TAAAAAAAATGTTA
Found at i:1478650 original size:65 final size:67
Alignment explanation
Indices: 1478578--1478724 Score: 160
Period size: 72 Copynumber: 2.1 Consensus size: 67
1478568 ATTAAATTTT
* *
1478578 AAAAAATAAATCAAAT-AGGGAAATATTAAATT-TTAAAA-AAAATGT-T-ATATAAAAAATGTT
1 AAAAAATAAAT-AAATGA-AGAAATATTAAATTCATAAAAGAAAAT-TATAATATAAAAAATGTT
1478638 AAAAG
63 AAAAG
1478643 AAAAAATAAAATAAATGAAGAAATATTAAATTGCATAAAAGAAAATTAATAAAATATAAAAAATG
1 AAAAAAT-AAATAAATGAAGAAATATTAAATT-CATAAAAGAAAATT-AT--AATATAAAAAATG
1478708 TTAAAAG
61 TTAAAAG
*
1478715 AGAAAATAAA
1 AAAAAATAAA
1478725 AATAAAACAA
Statistics
Matches: 69, Mismatches: 3, Indels: 14
0.80 0.03 0.16
Matches are distributed among these distances:
65 24 0.35
66 5 0.07
67 6 0.09
68 5 0.07
69 1 0.01
71 3 0.04
72 25 0.36
ACGTcount: A:0.65, C:0.01, G:0.09, T:0.24
Consensus pattern (67 bp):
AAAAAATAAATAAATGAAGAAATATTAAATTCATAAAAGAAAATTATAATATAAAAAATGTTAAA
AG
Found at i:1478741 original size:45 final size:42
Alignment explanation
Indices: 1478690--1478791 Score: 118
Period size: 40 Copynumber: 2.4 Consensus size: 42
1478680 AAAGAAAATT
*
1478690 AATAAAATATAAAAAATGTTAAAAGAGAAAATAAAAATAAAACAA
1 AATAAAATATAAAAAA-G--AAAAGAGAAAATAAAAACAAAACAA
** *
1478735 AAT-AAA-ATAAAAAAGAAGTGGGAAAATAAAAACAAAACAA
1 AATAAAATATAAAAAAGAAAAGAGAAAATAAAAACAAAACAA
1478775 AATAAAATAATAAAAAA
1 AATAAAAT-ATAAAAAA
1478792 AGAAGTGTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
40 24 0.48
41 3 0.06
42 1 0.02
43 16 0.32
44 3 0.06
45 3 0.06
ACGTcount: A:0.75, C:0.03, G:0.08, T:0.15
Consensus pattern (42 bp):
AATAAAATATAAAAAAGAAAAGAGAAAATAAAAACAAAACAA
Done.