Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007905.1 Hibiscus syriacus cultivar Beakdansim tig00110299_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: 2946335
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 14
Found at i:811662 original size:3 final size:3
Alignment explanation
Indices: 811620--811705 Score: 59
Period size: 3 Copynumber: 29.3 Consensus size: 3
811610 GGGTTATAAA
* * * *
811620 TAT TA- TAT TAT AAT TAT TAA TAT TA- TAT TAT AAC TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
811666 TAT AAC AAT TAA AAT TAT TAT TAG TAT TAT TAT TAA TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
811706 GCTTATGTTT
Statistics
Matches: 61, Mismatches: 20, Indels: 4
0.72 0.24 0.05
Matches are distributed among these distances:
2 4 0.07
3 57 0.93
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (3 bp):
TAT
Found at i:811666 original size:23 final size:20
Alignment explanation
Indices: 811613--811705 Score: 82
Period size: 20 Copynumber: 4.5 Consensus size: 20
811603 TTTGTCCGGG
*
811613 TTATAAATATTATATTATAA
1 TTATTAATATTATATTATAA
811633 TTATTAATATTATATTATAA
1 TTATTAATATTATATTATAA
* *
811653 CTATTATTA-T-TATTATAA
1 TTATTAATATTATATTATAA
** *
811671 CAATTAAAATTATTATTAGTATTA
1 TTATTAATATTA-TATTA-TA--A
811695 TTATTAATATT
1 TTATTAATATT
811706 GCTTATGTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
18 14 0.24
19 2 0.03
20 26 0.45
21 5 0.09
22 2 0.03
24 9 0.16
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (20 bp):
TTATTAATATTATATTATAA
Found at i:823944 original size:30 final size:31
Alignment explanation
Indices: 823882--823941 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
823872 GACTATTTTT
823882 TAAGTTTTGATCCTTAATGTTCGAGAAAAAC
1 TAAGTTTTGATCCTTAATGTTCGAGAAAAAC
* *
823913 TAAGTTTTGATCTTTAGTGTTCGAGAAAA
1 TAAGTTTTGATCCTTAATGTTCGAGAAAA
823942 CTAGGGGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.38
Consensus pattern (31 bp):
TAAGTTTTGATCCTTAATGTTCGAGAAAAAC
Found at i:829293 original size:28 final size:28
Alignment explanation
Indices: 829262--829352 Score: 76
Period size: 28 Copynumber: 3.1 Consensus size: 28
829252 ATTTTAGCAT
829262 AAAGATGCCACTAATGCAAGTTAGATGA
1 AAAGATGCCACTAATGCAAGTTAGATGA
* ** * *
829290 AAAGTTAAATGCCTACT-GTGCATTTTGGAAGA
1 AAAG----ATGCC-ACTAATGCAAGTTAGATGA
*
829322 AAAGGTGCCACTAATGCAAGTTAGATGA
1 AAAGATGCCACTAATGCAAGTTAGATGA
829350 AAA
1 AAA
829353 ATTAAATGTC
Statistics
Matches: 46, Mismatches: 11, Indels: 12
0.67 0.16 0.17
Matches are distributed among these distances:
27 3 0.07
28 21 0.46
32 19 0.41
33 3 0.07
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.24
Consensus pattern (28 bp):
AAAGATGCCACTAATGCAAGTTAGATGA
Found at i:829295 original size:60 final size:60
Alignment explanation
Indices: 829222--829596 Score: 513
Period size: 60 Copynumber: 6.2 Consensus size: 60
829212 GGAACTGCTA
* * * * *
829222 TTAGATGAAAAGTTAATTGCCTAATTGTGCATTTTAGCATAAAGATGCCACTAATGCAAG
1 TTAGATGAAAAGTTAAATGCCTAACTGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAG
*
829282 TTAGATGAAAAGTTAAATGCCT-ACTGTGCATTTTGGAAGAAAAGGTGCCACTAATGCAAG
1 TTAGATGAAAAGTTAAATGCCTAACTGTGCATTTTGGCAG-AAAGGTGCCACTAATGCAAG
* * * * *
829342 TTAGATGAAAAATTAAATGTCTAACTGTGCATTTTGACAGAAATGTGGCACTAATGCAAG
1 TTAGATGAAAAGTTAAATGCCTAACTGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAG
* * *
829402 TTAGATGAAAAGTTAAATGCCTAACTATGCATTTTGGTAGAAAGGTGCCACTAATTCAAG
1 TTAGATGAAAAGTTAAATGCCTAACTGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAG
* * *
829462 TTAGATGAAATA-TTAAATGTCTAACTGTGCATTTTGGCAGGAAGGTGCCACAAATGCAAG
1 TTAGATGAAA-AGTTAAATGCCTAACTGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAG
* * * *
829522 TTAGATGAAAAGTTCAATGCCTAA-TGGCGCATTTTGGCAAAAAGGTGCCACTAATACAAG
1 TTAGATGAAAAGTTAAATGCCTAACT-GTGCATTTTGGCAGAAAGGTGCCACTAATGCAAG
829582 TTAGATGAAAAGTTA
1 TTAGATGAAAAGTTA
829597 GAACAATGTA
Statistics
Matches: 276, Mismatches: 34, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
59 15 0.05
60 245 0.89
61 16 0.06
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (60 bp):
TTAGATGAAAAGTTAAATGCCTAACTGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAG
Found at i:829302 original size:32 final size:32
Alignment explanation
Indices: 829266--829360 Score: 83
Period size: 32 Copynumber: 3.1 Consensus size: 32
829256 TAGCATAAAG
829266 ATGCCACTAATGCAAGTTAGATGAAAAGTTAA
1 ATGCCACTAATGCAAGTTAGATGAAAAGTTAA
* ** * *
829298 ATGCCTACT-GTGCATTTTGGAAGAAAAG----
1 ATGCC-ACTAATGCAAGTTAGATGAAAAGTTAA
* *
829326 GTGCCACTAATGCAAGTTAGATGAAAAATTAA
1 ATGCCACTAATGCAAGTTAGATGAAAAGTTAA
829358 ATG
1 ATG
829361 TCTAACTGTG
Statistics
Matches: 44, Mismatches: 13, Indels: 12
0.64 0.19 0.17
Matches are distributed among these distances:
27 3 0.07
28 17 0.39
32 21 0.48
33 3 0.07
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (32 bp):
ATGCCACTAATGCAAGTTAGATGAAAAGTTAA
Found at i:836330 original size:60 final size:60
Alignment explanation
Indices: 836237--836669 Score: 645
Period size: 60 Copynumber: 7.2 Consensus size: 60
836227 AACTGCTCTA
* *
836237 AGATGAAAAATTAAATGCCTAACTTTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTT
1 AGATGAAAAGTTAAATGCCTAACTGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTT
* *
836297 AGATGAAAAGTTAAATGCCTAATTGTGCATTTTGGCAGAAAGGTGCCACTAACGCAAGTT
1 AGATGAAAAGTTAAATGCCTAACTGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTT
* * *
836357 AGATGAAAAGTTAAATGCCTAACTGTGCATTTTGACAGAAAGGTGGCACTAATGAAAGTT
1 AGATGAAAAGTTAAATGCCTAACTGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTT
** * * *
836417 AGATGAAAAGTTAAATGTATAACTGTGCATTTTGGTAGAATGGTGGCACTAATGCAAGTT
1 AGATGAAAAGTTAAATGCCTAACTGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTT
* * *
836477 AGATGAAAAGCTAAATGCCTAACTGTGTATTTTGGCAGAAAGGTGTCACTAATGCAAGTT
1 AGATGAAAAGTTAAATGCCTAACTGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTT
* * *
836537 AGATGAAAAGTTCAATGCCTAATTGTGCATTTTGGCAGAAAGGTACCACTAATGCAAGTT
1 AGATGAAAAGTTAAATGCCTAACTGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTT
* *
836597 AGATGAAAAGTTCAATGCCTAAC-GATGCATTTTGGCAGAAATGG-GCCACTAATGCAGGTT
1 AGATGAAAAGTTAAATGCCTAACTG-TGCATTTTGGCAGAAA-GGTGCCACTAATGCAAGTT
*
836657 AAATGAAAAGTTA
1 AGATGAAAAGTTA
836670 GAACAATGCA
Statistics
Matches: 338, Mismatches: 33, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
59 1 0.00
60 335 0.99
61 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (60 bp):
AGATGAAAAGTTAAATGCCTAACTGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTT
Found at i:836559 original size:30 final size:30
Alignment explanation
Indices: 836525--836618 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 30
836515 AAAGGTGTCA
836525 CTAATGCAAGTTAGATGAAAAGTTCAATGC
1 CTAATGCAAGTTAGATGAAAAGTTCAATGC
** * * * *
836555 CTAATTGTGCATTTTGGCA-GAAAGGTACCA---
1 CTAA---TGCAAGTTAG-ATGAAAAGTTCAATGC
836585 CTAATGCAAGTTAGATGAAAAGTTCAATGC
1 CTAATGCAAGTTAGATGAAAAGTTCAATGC
836615 CTAA
1 CTAA
836619 CGATGCATTT
Statistics
Matches: 44, Mismatches: 12, Indels: 16
0.61 0.17 0.22
Matches are distributed among these distances:
26 1 0.02
27 15 0.34
30 12 0.27
33 15 0.34
34 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (30 bp):
CTAATGCAAGTTAGATGAAAAGTTCAATGC
Found at i:844272 original size:21 final size:20
Alignment explanation
Indices: 844248--844311 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
844238 AACTTTGAAA
844248 AAATGATTTTCAAAGTTTGGT
1 AAATG-TTTTCAAAGTTTGGT
*
844269 AAATG-TTTC----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
844283 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
844304 AAATGTTT
1 AAATGTTT
844312 CTTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 4 0.12
16 4 0.12
19 4 0.12
20 7 0.21
21 10 0.29
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:844286 original size:35 final size:36
Alignment explanation
Indices: 844240--844361 Score: 176
Period size: 35 Copynumber: 3.4 Consensus size: 36
844230 TGGTAACCAA
844240 CTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTT
*
844277 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
844312 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
*
844349 -GTTGAAAAATGAT
1 CTTTGAAAAATGAT
844362 AATGGGATAA
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
35 36 0.46
36 14 0.18
37 28 0.36
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:844789 original size:16 final size:17
Alignment explanation
Indices: 844768--844799 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
844758 TTACTATTCA
844768 CGTGAATAGT-AAATTT
1 CGTGAATAGTGAAATTT
844784 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
844800 CGGTCGGCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:848866 original size:21 final size:20
Alignment explanation
Indices: 848842--848905 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
848832 AACTTTGAAA
848842 AAATGATTTTCAAAGTTTGGT
1 AAATG-TTTTCAAAGTTTGGT
*
848863 AAATG-TTTC----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
848877 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
848898 AAATGTTT
1 AAATGTTT
848906 CTTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 4 0.12
16 4 0.12
19 4 0.12
20 7 0.21
21 10 0.29
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:848880 original size:35 final size:36
Alignment explanation
Indices: 848834--848955 Score: 167
Period size: 35 Copynumber: 3.4 Consensus size: 36
848824 TGGTAACCAA
848834 CTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTT
*
848871 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
848906 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
* *
848943 -GTTAAAAAATGAT
1 CTTTGAAAAATGAT
848956 AATGGGATAA
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
35 36 0.47
36 13 0.17
37 28 0.36
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:851473 original size:12 final size:12
Alignment explanation
Indices: 851456--851483 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
851446 AAGTTTCCAC
851456 TTTATTACTTGA
1 TTTATTACTTGA
851468 TTTATTACTTGA
1 TTTATTACTTGA
851480 TTTA
1 TTTA
851484 CGACATGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.07, G:0.07, T:0.61
Consensus pattern (12 bp):
TTTATTACTTGA
Found at i:859223 original size:24 final size:24
Alignment explanation
Indices: 859191--859236 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
859181 TCTTCCAGAT
*
859191 GATGTATAAAACATTTATGTACAC
1 GATGTATAAAACATCTATGTACAC
859215 GATGTATAAAACATCTATGTAC
1 GATGTATAAAACATCTATGTAC
859237 CATGTCATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (24 bp):
GATGTATAAAACATCTATGTACAC
Found at i:860964 original size:31 final size:32
Alignment explanation
Indices: 860929--860989 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
860919 AATTATCATT
* **
860929 TTGGTCCCTAAATGTTTTC-AAAATTTATAAA
1 TTGGTCACTAAAACTTTTCTAAAATTTATAAA
*
860960 TTGGTCACTAAAACTTTTCTAAAGTTTATA
1 TTGGTCACTAAAACTTTTCTAAAATTTATA
860990 CTTTAGTCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 16 0.64
32 9 0.36
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (32 bp):
TTGGTCACTAAAACTTTTCTAAAATTTATAAA
Found at i:862489 original size:17 final size:18
Alignment explanation
Indices: 862456--862494 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
862446 ATGCAATTCC
862456 AATCAATCCCAAATCAA-
1 AATCAATCCCAAATCAAT
862473 AATCAAT-CCAAATTCAAT
1 AATCAATCCCAAA-TCAAT
862491 AATC
1 AATC
862495 CTTCATAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 5 0.25
17 11 0.55
18 4 0.20
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (18 bp):
AATCAATCCCAAATCAAT
Found at i:864252 original size:75 final size:75
Alignment explanation
Indices: 864167--864309 Score: 277
Period size: 75 Copynumber: 1.9 Consensus size: 75
864157 TATTACAGAT
*
864167 ACTACTCTTTAGATTCTCATATTTTTTAACTTAAATAATTAGATATAAATTGATAAAAGCTATAA
1 ACTACTCTTTAGATTCTCATATTTTTGAACTTAAATAATTAGATATAAATTGATAAAAGCTATAA
864232 ATTTACCGAG
66 ATTTACCGAG
864242 ACTACTCTTTAGATTCTCATATTTTTGAACTTAAATAATTAGATATAAATTGATAAAAGCTATAA
1 ACTACTCTTTAGATTCTCATATTTTTGAACTTAAATAATTAGATATAAATTGATAAAAGCTATAA
864307 ATT
66 ATT
864310 CATAGACGAG
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.41
Consensus pattern (75 bp):
ACTACTCTTTAGATTCTCATATTTTTGAACTTAAATAATTAGATATAAATTGATAAAAGCTATAA
ATTTACCGAG
Found at i:866734 original size:2 final size:2
Alignment explanation
Indices: 866729--866812 Score: 168
Period size: 2 Copynumber: 42.0 Consensus size: 2
866719 ACTATATACG
866729 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
866771 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
866813 TTCAGTCTTT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:866993 original size:13 final size:13
Alignment explanation
Indices: 866975--866999 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
866965 GATAGATGGG
866975 AATGCTTTCAGGA
1 AATGCTTTCAGGA
866988 AATGCTTTCAGG
1 AATGCTTTCAGG
867000 CTTTTTGAGG
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:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (13 bp):
AATGCTTTCAGGA
Found at i:870966 original size:20 final size:21
Alignment explanation
Indices: 870941--870981 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
870931 AATTTTCAAC
870941 CCAATGTG-GGTGCCAAACTT
1 CCAATGTGCGGTGCCAAACTT
870961 CCAATGTGCGGTGCCAAACTT
1 CCAATGTGCGGTGCCAAACTT
870982 TGTTTTGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (21 bp):
CCAATGTGCGGTGCCAAACTT
Found at i:872189 original size:13 final size:13
Alignment explanation
Indices: 872158--872191 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
872148 ATAATAGTAT
*
872158 TTTTAGTTTTAAA
1 TTTTATTTTTAAA
872171 -TTTATTTTTAAA
1 TTTTATTTTTAAA
872183 TTTTATTTT
1 TTTTATTTT
872192 AATTCAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (13 bp):
TTTTATTTTTAAA
Found at i:873689 original size:13 final size:13
Alignment explanation
Indices: 873671--873700 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
873661 TTCGAACACG
*
873671 AAGATGACTGCTT
1 AAGATGACTACTT
873684 AAGATGACTACTT
1 AAGATGACTACTT
873697 AAGA
1 AAGA
873701 GTGTTAACGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (13 bp):
AAGATGACTACTT
Found at i:884909 original size:12 final size:12
Alignment explanation
Indices: 884889--884932 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
884879 ATAACAAAGG
884889 AAATGAAAATAAT
1 AAAT-AAAATAAT
884902 AAATAAAATAAT
1 AAATAAAATAAT
884914 ATAAT-AAATAAT
1 A-AATAAAATAAT
*
884926 ATATAAA
1 AAATAAA
884933 CTTAGACTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 2 0.07
12 19 0.68
13 7 0.25
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (12 bp):
AAATAAAATAAT
Found at i:885049 original size:37 final size:37
Alignment explanation
Indices: 884990--885507 Score: 637
Period size: 37 Copynumber: 13.9 Consensus size: 37
884980 TATATATAAC
* *
884990 TTCAAAGACTATATATTATATATATGTTTTCAAAATGTT
1 TTCAAAAACTATATATTATATATA--TTTTCAAAATATT
*
885029 TTCAAAAA-TCGTATATTATATATATTTTCAAAATATT
1 TTCAAAAACT-ATATATTATATATATTTTCAAAATATT
*
885066 TTCAAAAACTATATATTATATATATGTTTTCAAAATGTT
1 TTCAAAAACTATATATTATATATA--TTTTCAAAATATT
* *
885105 TTCAAAAACCACATATTATATATATTTTCAAAATATT
1 TTCAAAAACTATATATTATATATATTTTCAAAATATT
*
885142 TTCAAAAACTATATATTATATATATGTTTTCAAAATGTT
1 TTCAAAAACTATATATTATATATA--TTTTCAAAATATT
885181 TTCAAAAACTATATATTATATATATTTTCAAAATATT
1 TTCAAAAACTATATATTATATATATTTTCAAAATATT
* * * *
885218 TTCAAAAACCATATATTATTTATATGTTTTAAAAAAAATGTT
1 TTCAAAAACTATATATTA--TATATATTTT---CAAAATATT
* * *
885260 TTCAAAAACCATATATTATATAAATTTTCAAAGTATT
1 TTCAAAAACTATATATTATATATATTTTCAAAATATT
*
885297 TTCAAAAACTATATA--ATATATA---T----ATGTT
1 TTCAAAAACTATATATTATATATATTTTCAAAATATT
885325 TTCAAAAACTATATATTATATATATTTTCAAAATATT
1 TTCAAAAACTATATATTATATATATTTTCAAAATATT
*
885362 TTCAAAAACTATATATTACATATATTTTCAAAATATT
1 TTCAAAAACTATATATTATATATATTTTCAAAATATT
* * *
885399 TT-AAAAACTATATATCATATATGTGTTTTCAAAATGTT
1 TTCAAAAACTATATAT--TATATATATTTTCAAAATATT
885437 TTCAAAAACTATATATTATATATA-TTTCAAAAATATT
1 TTCAAAAACTATATATTATATATATTTTC-AAAATATT
*
885474 TTCAAAAACTATATATTATATATGTTTTCAAAAT
1 TTCAAAAACTATATATTATATATATTTTCAAAAT
885508 TTTATGTATA
Statistics
Matches: 419, Mismatches: 35, Indels: 52
0.83 0.07 0.10
Matches are distributed among these distances:
28 18 0.04
30 7 0.02
32 1 0.00
33 1 0.00
35 6 0.01
36 17 0.04
37 199 0.47
38 25 0.06
39 112 0.27
40 8 0.02
42 25 0.06
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (37 bp):
TTCAAAAACTATATATTATATATATTTTCAAAATATT
Found at i:885070 original size:76 final size:75
Alignment explanation
Indices: 884990--885507 Score: 665
Period size: 76 Copynumber: 7.0 Consensus size: 75
884980 TATATATAAC
* *
884990 TTCAAAGACTATATATTATATATATGTTTTCAAAATGTTTTCAAAAATCGTATATTATATATATT
1 TTCAAAAACTATATATTATATATATGTTTTCAAAATGTTTTCAAAAA-CATATATTATATATATT
885055 TTCAAAATATT
65 TTCAAAATATT
*
885066 TTCAAAAACTATATATTATATATATGTTTTCAAAATGTTTTCAAAAACCACATATTATATATATT
1 TTCAAAAACTATATATTATATATATGTTTTCAAAATGTTTTCAAAAA-CATATATTATATATATT
885131 TTCAAAATATT
65 TTCAAAATATT
885142 TTCAAAAACTATATATTATATATATGTTTTCAAAATGTTTTCAAAAACTATATATTATATATATT
1 TTCAAAAACTATATATTATATATATGTTTTCAAAATGTTTTCAAAAAC-ATATATTATATATATT
885207 TTCAAAATATT
65 TTCAAAATATT
* * * *
885218 TTCAAAAACCATATATTATTTATATGTTTTAAAAAAAATGTTTTCAAAAACCATATATTATATAA
1 TTCAAAAACTATATATTATATATATGTTTT---CAAAATGTTTTCAAAAA-CATATATTATATAT
*
885283 ATTTTCAAAGTATT
62 ATTTTCAAAATATT
885297 TTCAAAAACTATATA--ATATATA-----T----ATGTTTTCAAAAACTATATATTATATATATT
1 TTCAAAAACTATATATTATATATATGTTTTCAAAATGTTTTCAAAAAC-ATATATTATATATATT
885351 TTCAAAATATT
65 TTCAAAATATT
* * * *
885362 TTCAAAAACTATATATTACATATA--TTTTCAAAATATTTT-AAAAACTATATATCATATATGTG
1 TTCAAAAACTATATATTATATATATGTTTTCAAAATGTTTTCAAAAAC-ATATAT--TATATATA
*
885424 TTTTCAAAATGTT
63 TTTTCAAAATATT
* *
885437 TTCAAAAACTATATATTATATATA---TTTCAAAAATATTTTCAAAAACTATATATTATATATGT
1 TTCAAAAACTATATATTATATATATGTTTTC-AAAATGTTTTCAAAAAC-ATATATTATATATAT
885499 TTTCAAAAT
64 TTTCAAAAT
885508 TTTATGTATA
Statistics
Matches: 402, Mismatches: 21, Indels: 40
0.87 0.05 0.09
Matches are distributed among these distances:
64 1 0.00
65 53 0.13
67 6 0.01
70 1 0.00
72 1 0.00
73 13 0.03
74 27 0.07
75 52 0.13
76 186 0.46
77 6 0.01
79 55 0.14
80 1 0.00
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (75 bp):
TTCAAAAACTATATATTATATATATGTTTTCAAAATGTTTTCAAAAACATATATTATATATATTT
TCAAAATATT
Found at i:885340 original size:30 final size:28
Alignment explanation
Indices: 885295--885357 Score: 103
Period size: 26 Copynumber: 2.3 Consensus size: 28
885285 TTTCAAAGTA
885295 TTTTCAAAAACTATATAATATATATATG
1 TTTTCAAAAACTATATAATATATATATG
*
885323 TTTTCAAAAACTATAT-AT-TATATATA
1 TTTTCAAAAACTATATAATATATATATG
885349 TTTTCAAAA
1 TTTTCAAAA
885358 TATTTTCAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
26 16 0.47
27 2 0.06
28 16 0.47
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (28 bp):
TTTTCAAAAACTATATAATATATATATG
Found at i:885344 original size:26 final size:28
Alignment explanation
Indices: 885293--885357 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
885283 ATTTTCAAAG
885293 TATTTTCAAAAACTATATAATATATATA
1 TATTTTCAAAAACTATATAATATATATA
*
885321 TGTTTTCAAAAACTATAT-AT-TATATA
1 TATTTTCAAAAACTATATAATATATATA
885347 TATTTTCAAAA
1 TATTTTCAAAA
885358 TATTTTCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
26 16 0.46
27 2 0.06
28 17 0.49
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.45
Consensus pattern (28 bp):
TATTTTCAAAAACTATATAATATATATA
Found at i:885360 original size:11 final size:11
Alignment explanation
Indices: 885346--885404 Score: 50
Period size: 11 Copynumber: 5.1 Consensus size: 11
885336 TATATTATAT
885346 ATATTTTCAAA
1 ATATTTTCAAA
885357 ATATTTTCAAAA
1 ATATTTTC-AAA
*
885369 ACTATATATT-ACAT
1 A-TAT-T-TTCA-AA
885383 ATATTTTCAAA
1 ATATTTTCAAA
885394 ATATTTT-AAA
1 ATATTTTCAAA
885404 A
1 A
885405 ACTATATATC
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
10 4 0.10
11 18 0.45
12 6 0.15
13 7 0.17
14 3 0.08
15 2 0.05
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.44
Consensus pattern (11 bp):
ATATTTTCAAA
Found at i:885385 original size:65 final size:65
Alignment explanation
Indices: 885255--885461 Score: 236
Period size: 65 Copynumber: 3.0 Consensus size: 65
885245 TTTAAAAAAA
* * * *
885255 ATGTTTTCAAAAACCATATATTATATAAATTTTCAAAGTATTTTCAAAAACTATATAATATATAT
1 ATGTTTTCAAAAACTATATATTATATATATTTTCAAAATATTTTCAAAAACTATATATTATATAT
885320 ATGTTTTCAAAAACTATATATTATATATATTTTCAAAATATTTTCAAAAACTATATATTACATAT
1 ATGTTTTCAAAAACTATATATTATATATATTTTCAAAATATTTTCAAAAACTATATATT--ATAT
885385 ATTTT
64 A---T
* * * *
885390 CAAAATATTTT-AAAAACTATATATCATATATGTGTTTTCAAAATGTTTTCAAAAACTATATATT
1 ----ATGTTTTCAAAAACTATATAT--TATATATATTTTCAAAATATTTTCAAAAACTATATATT
885454 ATATAT
60 ATATAT
885460 AT
1 AT
885462 TTCAAAAATA
Statistics
Matches: 123, Mismatches: 8, Indels: 21
0.81 0.05 0.14
Matches are distributed among these distances:
65 55 0.45
66 2 0.02
67 5 0.04
70 2 0.02
73 18 0.15
74 6 0.05
75 35 0.28
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (65 bp):
ATGTTTTCAAAAACTATATATTATATATATTTTCAAAATATTTTCAAAAACTATATATTATATAT
Found at i:885529 original size:75 final size:74
Alignment explanation
Indices: 885323--885507 Score: 293
Period size: 75 Copynumber: 2.5 Consensus size: 74
885313 TATATATATG
*
885323 TTTTCAAAAACTATATATTATATATATTTTCAAAATATTTTCAAAAACTATATATTACATATATT
1 TTTTCAAAAACTATATATTATATATGTTTTCAAAATATTTTCAAAAACTATATATTACATATATT
885388 TTCAAAATA
66 TTCAAAATA
* * *
885397 TTTT-AAAAACTATATATCATATATGTGTTTTCAAAATGTTTTCAAAAACTATATATTATATATA
1 TTTTCAAAAACTATATAT--TATATATGTTTTCAAAATATTTTCAAAAACTATATATTACATATA
885461 -TTTCAAAAATA
64 TTTTC-AAAATA
885472 TTTTCAAAAACTATATATTATATATGTTTTCAAAAT
1 TTTTCAAAAACTATATATTATATATGTTTTCAAAAT
885508 TTTATGTATA
Statistics
Matches: 102, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
73 13 0.13
74 25 0.25
75 51 0.50
76 13 0.13
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (74 bp):
TTTTCAAAAACTATATATTATATATGTTTTCAAAATATTTTCAAAAACTATATATTACATATATT
TTCAAAATA
Found at i:890421 original size:17 final size:17
Alignment explanation
Indices: 890399--890492 Score: 79
Period size: 17 Copynumber: 5.4 Consensus size: 17
890389 GTACTAAATG
890399 AAAGAAAATTGAATTCA
1 AAAGAAAATTGAATTCA
*
890416 AAAGAAAAGTACTGAA-T-G
1 AAAGAAAA-T--TGAATTCA
890434 AAAGAAAATTGAATTCA
1 AAAGAAAATTGAATTCA
*
890451 AAAGAAAAGTACTGAA-T-G
1 AAAGAAAA-T--TGAATTCA
*
890469 AAAGAAAATTGAGTTCA
1 AAAGAAAATTGAATTCA
890486 AAAGAAA
1 AAAGAAA
890493 TGAAATAAGA
Statistics
Matches: 62, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
15 7 0.11
16 2 0.03
17 25 0.40
18 18 0.29
19 2 0.03
20 8 0.13
ACGTcount: A:0.59, C:0.05, G:0.17, T:0.19
Consensus pattern (17 bp):
AAAGAAAATTGAATTCA
Found at i:890428 original size:35 final size:35
Alignment explanation
Indices: 890387--890492 Score: 194
Period size: 35 Copynumber: 3.0 Consensus size: 35
890377 TGATAAAAAG
*
890387 AAGTACTAAATGAAAGAAAATTGAATTCAAAAGAA
1 AAGTACTGAATGAAAGAAAATTGAATTCAAAAGAA
890422 AAGTACTGAATGAAAGAAAATTGAATTCAAAAGAA
1 AAGTACTGAATGAAAGAAAATTGAATTCAAAAGAA
*
890457 AAGTACTGAATGAAAGAAAATTGAGTTCAAAAGAA
1 AAGTACTGAATGAAAGAAAATTGAATTCAAAAGAA
890492 A
1 A
890493 TGAAATAAGA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 69 1.00
ACGTcount: A:0.58, C:0.06, G:0.17, T:0.20
Consensus pattern (35 bp):
AAGTACTGAATGAAAGAAAATTGAATTCAAAAGAA
Found at i:897635 original size:12 final size:13
Alignment explanation
Indices: 897613--897652 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
897603 ATAACAAAGG
897613 TAATGAAAATAATA
1 TAAT-AAAATAATA
897627 -AATAAAATAATA
1 TAATAAAATAATA
897639 TAAT-AAATAATA
1 TAATAAAATAATA
897651 TA
1 TA
897653 TATACTTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 19 0.76
13 6 0.24
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (13 bp):
TAATAAAATAATA
Found at i:897735 original size:37 final size:37
Alignment explanation
Indices: 897694--898055 Score: 162
Period size: 37 Copynumber: 10.8 Consensus size: 37
897684 TTTTTAAAAA
897694 AAAAACTATATAATATATATATATTTAAAATATTTTC
1 AAAAACTATATAATATATATATATTTAAAATATTTTC
*
897731 AAAAAC--TAT--T-TAT-TATA--T-AAATGTTTTC
1 AAAAACTATATAATATATATATATTTAAAATATTTTC
* * * *
897759 AAAAACCATATATTATATATAT-TTTCAAAA-ACTAT-
1 AAAAACTATATAATATATATATATTT-AAAATATTTTC
** * *
897794 -ATTA-TATAT-ATATATATATATTCAAAATGTTTTC
1 AAAAACTATATAATATATATATATTTAAAATATTTTC
*
897828 AAAAACTATAT-AT-TATATATTTTTCAAAATATTTTC
1 AAAAACTATATAATATATATATATTT-AAAATATTTTC
*
897864 AAAAAC--TAT-ATAT-TATATA--T---AT-GTTTC
1 AAAAACTATATAATATATATATATTTAAAATATTTTC
* * * * *
897891 AAAAACCATATATTATATAAAT-TTTCAAAGTATTTTT
1 AAAAACTATATAATATATATATATTT-AAAATATTTTC
897928 AAAAAC--TATAATATATATATA--T---ATA---T-
1 AAAAACTATATAATATATATATATTTAAAATATTTTC
* * * * *
897954 ATATA-TATAT-ATATATATATATTCAAAATGTTTTT
1 AAAAACTATATAATATATATATATTTAAAATATTTTC
*
897989 AAAAACTATATATTATATATAT-TTTCAAAATATTTTC
1 AAAAACTATATAATATATATATATTT-AAAATATTTTC
* *
898026 AAAAACTATATATTACATATAT-TTTCAAAA
1 AAAAACTATATAATATATATATATTT-AAAA
898056 AGAATGTATC
Statistics
Matches: 244, Mismatches: 38, Indels: 86
0.66 0.10 0.23
Matches are distributed among these distances:
26 14 0.06
27 14 0.06
28 17 0.07
29 4 0.02
30 8 0.03
31 10 0.04
32 19 0.08
33 12 0.05
34 17 0.07
35 31 0.13
36 33 0.14
37 65 0.27
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.44
Consensus pattern (37 bp):
AAAAACTATATAATATATATATATTTAAAATATTTTC
Found at i:897757 original size:28 final size:28
Alignment explanation
Indices: 897721--897820 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
897711 TATATATTTA
897721 AAATATTTTCAAAAACTATTTATTATAT
1 AAATATTTTCAAAAACTATTTATTATAT
* * *
897749 AAATGTTTTCAAAAACCATATATTATAT
1 AAATATTTTCAAAAACTATTTATTATAT
897777 --ATATTTTCAAAAACTATATTATATATAT
1 AAATATTTTCAAAAACTAT-TTAT-TATAT
*
897805 ATATATATATTCAAAA
1 A-A-ATATTTTCAAAA
897821 TGTTTTCAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
26 15 0.25
27 3 0.05
28 30 0.51
32 11 0.19
ACGTcount: A:0.48, C:0.08, G:0.01, T:0.43
Consensus pattern (28 bp):
AAATATTTTCAAAAACTATTTATTATAT
Found at i:897890 original size:27 final size:26
Alignment explanation
Indices: 897856--897919 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 26
897846 ATTTTTCAAA
*
897856 ATATTTTCAAAAACTATATATTATAT
1 ATATTTTCAAAAACCATATATTATAT
897882 ATATGTTTCAAAAACCATATATTATAT
1 ATAT-TTTCAAAAACCATATATTATAT
*
897909 AAATTTTCAAA
1 ATATTTTCAAA
897920 GTATTTTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
26 11 0.31
27 24 0.69
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (26 bp):
ATATTTTCAAAAACCATATATTATAT
Found at i:897945 original size:2 final size:2
Alignment explanation
Indices: 897934--897975 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
897924 TTTTAAAAAC
897934 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
897975 T
1 T
897976 TCAAAATGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:898071 original size:26 final size:26
Alignment explanation
Indices: 898018--898083 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
898008 TATTTTCAAA
* *
898018 ATATTTTCAAAAACTATATATTACAT
1 ATATTTTCAAAAACAATATATCACAT
* * *
898044 ATATTTTCAAAAAGAATGTATCATAT
1 ATATTTTCAAAAACAATATATCACAT
898070 ATATGTTTTCAAAA
1 ATA--TTTTCAAAA
898084 TGTTTTCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
26 24 0.73
28 9 0.27
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (26 bp):
ATATTTTCAAAAACAATATATCACAT
Found at i:898098 original size:102 final size:100
Alignment explanation
Indices: 897796--898157 Score: 373
Period size: 102 Copynumber: 3.6 Consensus size: 100
897786 AAAACTATAT
* *
897796 TATATATATATATATATATTCAAAATGTTTTCAAAAACTATATATTATATAT-TTTTC-AAAATA
1 TATATAT-TATATATATTTTCAAAATATTTTCAAAAACTATATATTATATATATTTTCAAAAATA
* * * *
897859 TTTTCAAAAACTATATATTAT-ATATATG-TTTCAAAAAC
65 TTATC--ATA-TATATATTTTCA-AAATGTTTTCAAAAAC
* * * * * * *
897897 CATATATTATATAAATTTTCAAAGTATTTTTAAAAACTATA-A-TATATATATATAT-ATATATA
1 TATATATTATATATATTTTCAAAATATTTTCAAAAACTATATATTATATATAT-TTTCAAAAATA
* *
897959 TATAT-ATATATATATATTCAAAATGTTTTTAAAAAC
65 T-TATCATATATATATTTTCAAAATGTTTTCAAAAAC
* *
897995 TATATATTATATATATTTTCAAAATATTTTCAAAAACTATATATTACATATATTTTCAAAAAGAA
1 TATATATTATATATATTTTCAAAATATTTTCAAAAACTATATATTATATATATTTTCAAAAA-TA
*
898060 TGTATCATATATATGTTTTCAAAATGTTTTCAAAAAC
65 T-TATCATATATATATTTTCAAAATGTTTTCAAAAAC
* * * *
898097 TATATATTAAATATATTTCCAAAATAAATTT-AAAAACTATATATTATATATGTTTTCAAAA
1 TATATATTATATATATTTTCAAAAT-ATTTTCAAAAACTATATATTATATATATTTTCAAAA
898158 TTTTATGTAT
Statistics
Matches: 216, Mismatches: 33, Indels: 23
0.79 0.12 0.08
Matches are distributed among these distances:
97 12 0.06
98 56 0.26
99 5 0.02
100 47 0.22
101 13 0.06
102 79 0.37
103 4 0.02
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.44
Consensus pattern (100 bp):
TATATATTATATATATTTTCAAAATATTTTCAAAAACTATATATTATATATATTTTCAAAAATAT
TATCATATATATATTTTCAAAATGTTTTCAAAAAC
Found at i:898099 original size:163 final size:158
Alignment explanation
Indices: 897791--898112 Score: 484
Period size: 161 Copynumber: 2.0 Consensus size: 158
897781 TTTCAAAAAC
897791 TATATTATATATATATATATATATTCAAAATGTTTTCAAAAACTATATATTATATATTTTTCAAA
1 TATATTATATATATATATATATATTCAAAATGTTTTCAAAAACTATATATTATATATTTTTCAAA
* * *
897856 ATATTTTCAAAAACTATATATTATATATATGTTTCAAAAACCATATATTATATAAATTTTCAAAG
66 ATATTTTCAAAAACTATATATTACATATATGTTTCAAAAACAATATATTATATAAATTTTCAAAA
* *
897921 TATTTTTAAAAACTATAATATATATATATA
131 TATTTTCAAAAACTAT-ATAT-TAAATATA
*
897951 TATATATATATATATATATATATATTCAAAATGTTTTTAAAAACTATATATTATATATATTTTCA
1 TATAT-TATATATATATATATATATTCAAAATGTTTTCAAAAACTATATATTATATAT-TTTTCA
* * **
898016 AAATATTTTCAAAAACTATATATTACATATAT-TTTCAAAAAGAATGTATCATATATATGTTTTC
64 AAATATTTTCAAAAACTATATATTACATATATGTTTCAAAAACAATATAT--TATATAAATTTTC
*
898080 AAAATGTTTTCAAAAACTATATATTAAATATA
127 AAAATATTTTCAAAAACTATATATTAAATATA
898112 T
1 T
898113 TTCCAAAATA
Statistics
Matches: 147, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
160 5 0.03
161 73 0.50
162 41 0.28
163 28 0.19
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (158 bp):
TATATTATATATATATATATATATTCAAAATGTTTTCAAAAACTATATATTATATATTTTTCAAA
ATATTTTCAAAAACTATATATTACATATATGTTTCAAAAACAATATATTATATAAATTTTCAAAA
TATTTTCAAAAACTATATATTAAATATA
Found at i:898138 original size:65 final size:65
Alignment explanation
Indices: 898003--898141 Score: 183
Period size: 65 Copynumber: 2.1 Consensus size: 65
897993 ACTATATATT
* * * *
898003 ATATATATTTTCAAAATATTTTCAAAAACTATATATTACATATATTTTCAAAAAGAATGTATCAT
1 ATATATATTTTCAAAATATTTTCAAAAACTATATATTAAATATATTTCCAAAAAGAATGTATAAA
* * *
898068 ATATATGTTTTCAAAATGTTTTCAAAAACTATATATTAAATATATTTCCAAAATA-AATTTA-AA
1 ATATATATTTTCAAAATATTTTCAAAAACTATATATTAAATATATTTCCAAAA-AGAATGTATAA
898131 A
65 A
898132 ACTATATATT
1 A-TATATATT
898142 ATATATGTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
64 2 0.03
65 61 0.95
66 1 0.02
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.42
Consensus pattern (65 bp):
ATATATATTTTCAAAATATTTTCAAAAACTATATATTAAATATATTTCCAAAAAGAATGTATAAA
Found at i:901496 original size:3 final size:3
Alignment explanation
Indices: 901490--901565 Score: 113
Period size: 3 Copynumber: 25.7 Consensus size: 3
901480 TTCATTTGAA
901490 TAT TAT T-T ATAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
901534 TAT TA- TAT TAT TAT TATT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TA
901566 CTAAATAATT
Statistics
Matches: 68, Mismatches: 0, Indels: 10
0.87 0.00 0.13
Matches are distributed among these distances:
2 5 0.07
3 59 0.87
4 4 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:902113 original size:13 final size:12
Alignment explanation
Indices: 902059--902119 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 12
902049 AGTATTATTG
902059 TTATTTTATATA
1 TTATTTTATATA
902071 TATATATATATATATA
1 T-TAT-T-T-TATATA
*
902087 TATATATATATATA
1 T-TAT-TTTATATA
902101 TTGATTTTATATA
1 TT-ATTTTATATA
902114 TTATTT
1 TTATTT
902120 ATTTTTATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
12 5 0.12
13 13 0.31
14 10 0.24
15 1 0.02
16 13 0.31
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (12 bp):
TTATTTTATATA
Found at i:902114 original size:2 final size:2
Alignment explanation
Indices: 902065--902101 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
902055 ATTGTTATTT
902065 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
902102 TGATTTTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:902998 original size:26 final size:27
Alignment explanation
Indices: 902946--903001 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
902936 AATTCTTTTC
*
902946 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATAC-TATTA
* *
902974 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCAAAATATTTATATATACTATTA
903000 TT
1 TT
903002 AATATTTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 7 0.28
28 18 0.72
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATACTATTA
Found at i:908133 original size:16 final size:16
Alignment explanation
Indices: 908109--908142 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
908099 ACAATCATTC
*
908109 TTTACATTCTTTATAT
1 TTTACATTCATTATAT
*
908125 TTTAGATTCATTATAT
1 TTTACATTCATTATAT
908141 TT
1 TT
908143 CATTTATTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.09, G:0.03, T:0.62
Consensus pattern (16 bp):
TTTACATTCATTATAT
Found at i:911583 original size:35 final size:35
Alignment explanation
Indices: 911543--911614 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 35
911533 ATGCTTGAAG
911543 AAGAAAAAAT-AA-AAGAAAAGAAAAAAAGAAAAGAA
1 AAGAAAAAATGAAGAA-AAAAG-AAAAAAGAAAAGAA
911578 AAGAAAAAATGAAGAAAAAAGAAAAAAGAAAAGAA
1 AAGAAAAAATGAAGAAAAAAGAAAAAAGAAAAGAA
911613 AA
1 AA
911615 ATGTTGAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
35 26 0.74
36 7 0.20
37 2 0.06
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (35 bp):
AAGAAAAAATGAAGAAAAAAGAAAAAAGAAAAGAA
Found at i:911592 original size:29 final size:29
Alignment explanation
Indices: 911560--911642 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
911550 AATAAAAGAA
911560 AAGAAAAAAAGAAAAGAAAAGAAAAAATG
1 AAGAAAAAAAGAAAAGAAAAGAAAAAATG
*
911589 AAGAAAAAAGAAAAAAGAAAAG-AAAAATG
1 AAGAAAAAA-AGAAAAGAAAAGAAAAAATG
**
911618 TTGAAAAAAAGAAAA-AAATAGAAAA
1 AAGAAAAAAAGAAAAGAAA-AGAAAA
911643 GGAGGGTCAG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
27 3 0.06
28 7 0.15
29 26 0.55
30 11 0.23
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (29 bp):
AAGAAAAAAAGAAAAGAAAAGAAAAAATG
Found at i:911615 original size:18 final size:17
Alignment explanation
Indices: 911543--911614 Score: 101
Period size: 18 Copynumber: 4.1 Consensus size: 17
911533 ATGCTTGAAG
*
911543 AAGAAAAAATAAAAGAA
1 AAGAAAAAAGAAAAGAA
911560 AAGAAAAAAAGAAAAGAA
1 AAG-AAAAAAGAAAAGAA
911578 AAGAAAAAATGAAGAA-AA
1 AAGAAAAAA-GAA-AAGAA
911596 AAGAAAAAAGAAAAGAA
1 AAGAAAAAAGAAAAGAA
911613 AA
1 AA
911615 ATGTTGAAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 8
0.85 0.02 0.14
Matches are distributed among these distances:
16 2 0.04
17 16 0.32
18 30 0.60
19 2 0.04
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (17 bp):
AAGAAAAAAGAAAAGAA
Found at i:911626 original size:30 final size:31
Alignment explanation
Indices: 911560--911634 Score: 104
Period size: 30 Copynumber: 2.5 Consensus size: 31
911550 AATAAAAGAA
911560 AAGAAAAAAAG--AAAAGAAAAGAAAAAATG
1 AAGAAAAAAAGAAAAAAGAAAAGAAAAAATG
911589 AAG-AAAAAAGAAAAAAGAAAAG-AAAAATG
1 AAGAAAAAAAGAAAAAAGAAAAGAAAAAATG
**
911618 TTGAAAAAAAGAAAAAA
1 AAGAAAAAAAGAAAAAA
911635 ATAGAAAAGG
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
28 7 0.17
29 11 0.27
30 23 0.56
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (31 bp):
AAGAAAAAAAGAAAAAAGAAAAGAAAAAATG
Found at i:911632 original size:5 final size:5
Alignment explanation
Indices: 911548--911614 Score: 63
Period size: 5 Copynumber: 13.8 Consensus size: 5
911538 TGAAGAAGAA
*
911548 AAAAT AAAAG AAAAG -AAA- AAAAG AAAAG AAAAG AAAA- AATGAAG AAAA-
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA--AAG AAAAG
911596 AAGAA- AAAAG AAAAG AAAA
1 AA-AAG AAAAG AAAAG AAAA
911615 ATGTTGAAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 14
0.78 0.01 0.20
Matches are distributed among these distances:
4 12 0.22
5 38 0.70
6 2 0.04
7 2 0.04
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:911634 original size:7 final size:7
Alignment explanation
Indices: 911558--911609 Score: 54
Period size: 7 Copynumber: 7.3 Consensus size: 7
911548 AAAATAAAAG
911558 AAAAGAA
1 AAAAGAA
*
911565 AAAA-AG
1 AAAAGAA
911571 AAAAGAA
1 AAAAGAA
911578 AAGAA-AA
1 AA-AAGAA
911585 AATGAAGAA
1 AA--AAGAA
911594 AAAAGAA
1 AAAAGAA
911601 AAAAGAA
1 AAAAGAA
911608 AA
1 AA
911610 GAAAAATGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
6 5 0.13
7 25 0.64
8 5 0.13
9 4 0.10
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (7 bp):
AAAAGAA
Found at i:911641 original size:18 final size:17
Alignment explanation
Indices: 911546--911642 Score: 79
Period size: 18 Copynumber: 5.2 Consensus size: 17
911536 CTTGAAGAAG
*
911546 AAAAAATAAAAGAAAAGA
1 AAAAAAGAAAA-AAAAGA
911564 AAAAAAGAAAAGAAAAGA
1 AAAAAAGAAAA-AAAAGA
*
911582 AAAAATGAAGAAAAAAG-
1 AAAAAAGAA-AAAAAAGA
911599 AAAAAAGAAAAGAAAAATGTTGA
1 AAAAAAG-AAA-AAAAA----GA
911622 AAAAAAGAAAAAAATAGA
1 AAAAAAGAAAAAAA-AGA
911640 AAA
1 AAA
911643 GGAGGGTCAG
Statistics
Matches: 67, Mismatches: 3, Indels: 18
0.76 0.03 0.20
Matches are distributed among these distances:
17 7 0.10
18 42 0.63
19 2 0.03
21 4 0.06
22 5 0.07
23 7 0.10
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.06
Consensus pattern (17 bp):
AAAAAAGAAAAAAAAGA
Found at i:912012 original size:18 final size:18
Alignment explanation
Indices: 911989--912023 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
911979 CAAGTTTATC
911989 TTTTTGAAATTCAATTTA
1 TTTTTGAAATTCAATTTA
912007 TTTTTGAAATTCAATTT
1 TTTTTGAAATTCAATTT
912024 GTTTCACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (18 bp):
TTTTTGAAATTCAATTTA
Found at i:913450 original size:122 final size:122
Alignment explanation
Indices: 913302--913843 Score: 881
Period size: 122 Copynumber: 4.4 Consensus size: 122
913292 CATTCGATGA
* *
913302 ATCAACTTTTCCAAAGAAGTTCATAATGAGAATAACTTATCTGAAGAGGAAGAAGAAGTTCATAA
1 ATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAA
*
913367 TGAGAAGAGCTTGTTCAACCTTTTGTATGACTCTATCGCAGAAGGAGATAGATCAGC
66 TGAGAAGAGCTTGTTCAACCTTTTGTATGACTCTATCACAGAAGGAGATAGATCAGC
913424 ATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAA
1 ATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAA
* * *
913489 TGAGAAGAGCTTGTTCAACCTTTTGTATGACTATATCGCAGAAGGATATAGATCAGC
66 TGAGAAGAGCTTGTTCAACCTTTTGTATGACTCTATCACAGAAGGAGATAGATCAGC
*
913546 ATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTTATCAGAAGAGGAAGAAGAAGTTCATAA
1 ATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAA
*
913611 TGAGAAGAGCTTGTTCAACCTTTTGTATGACTCTATCACAGAAGGAGATAGATCAAC
66 TGAGAAGAGCTTGTTCAACCTTTTGTATGACTCTATCACAGAAGGAGATAGATCAGC
* *
913668 ATCAACTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAG-AAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCAT
* * * *
913733 GATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATATACCAGC
64 AATGAGAAGAGCTTGTTCAACCTTTTGTATGACTCTATCACAGAAGGAGATAGATCAGC
* * *
913792 ATCAACATTTT-CAGA-AGTGTTCATAATGAGAAGAACTCATCTGAAGAAGAAG
1 ATCAAC-TTTTCCAGAGA-AGTTCATAATGAGAAGAACTTATCTGAAGAGGAAG
913844 GAGCAAAACT
Statistics
Matches: 396, Mismatches: 20, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
122 257 0.65
123 54 0.14
124 81 0.20
125 4 0.01
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (122 bp):
ATCAACTTTTCCAGAGAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAA
TGAGAAGAGCTTGTTCAACCTTTTGTATGACTCTATCACAGAAGGAGATAGATCAGC
Found at i:914090 original size:3 final size:3
Alignment explanation
Indices: 914084--914162 Score: 110
Period size: 3 Copynumber: 26.7 Consensus size: 3
914074 TTCATTTGAA
*
914084 TAT TAT T-T ATAT T-T TAT TAT TAT TAT AAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
914128 TAT TAT TA- TAT TAT TATT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TA
914163 CTAAATAATT
Statistics
Matches: 69, Mismatches: 2, Indels: 10
0.85 0.02 0.12
Matches are distributed among these distances:
2 5 0.07
3 60 0.87
4 4 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:914173 original size:27 final size:26
Alignment explanation
Indices: 914093--914173 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 26
914083 ATATTATTTA
* *
914093 TATT-TTATTATTATTATAATTATTAT
1 TATTATTATTATTATTATAAATAAT-T
* *
914119 TATTATTATTATTATTATATTATTATT
1 TATTATTATTATTATTATA-AATAATT
914146 TATTATTATTATTATTACTAAATAATT
1 TATTATTATTATTATTA-TAAATAATT
914173 T
1 T
914174 TATTTACAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
26 4 0.09
27 38 0.83
28 4 0.09
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (26 bp):
TATTATTATTATTATTATAAATAATT
Found at i:915441 original size:23 final size:22
Alignment explanation
Indices: 915424--915474 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
915414 TTATAAGTAT
915424 TATTGTTATTTATATATATATA
1 TATTGTTATTTATATATATATA
* *
915446 TATTGAT-TTTATATAT-TATT
1 TATTGTTATTTATATATATATA
*
915466 TATTTTTAT
1 TATTGTTAT
915475 ATGTTCTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 8 0.33
21 10 0.42
22 6 0.25
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (22 bp):
TATTGTTATTTATATATATATA
Found at i:915460 original size:17 final size:16
Alignment explanation
Indices: 915438--915476 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
915428 GTTATTTATA
915438 TATATATATATTGATTT
1 TATATAT-TATTGATTT
*
915455 TATATATTATTTATTT
1 TATATATTATTGATTT
915471 T-TATAT
1 TATATAT
915477 GTTCTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.24
16 9 0.43
17 7 0.33
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (16 bp):
TATATATTATTGATTT
Found at i:915578 original size:12 final size:12
Alignment explanation
Indices: 915563--915591 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
915553 CTATCTATAA
915563 ATTTTATAAATT
1 ATTTTATAAATT
915575 A-TTTATAAATT
1 ATTTTATAAATT
915586 ATTTTA
1 ATTTTA
915592 ATTATGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTTTATAAATT
Found at i:918462 original size:15 final size:16
Alignment explanation
Indices: 918424--918464 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
918414 TTAGAGCCTC
*
918424 TGAATCATTCAGCATT
1 TGAATCATTCAGCACT
*
918440 TGAATCATTCAGCGCT
1 TGAATCATTCAGCACT
918456 T-AATCATTC
1 TGAATCATTC
918465 TGAAGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Found at i:918670 original size:30 final size:30
Alignment explanation
Indices: 918636--918699 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
918626 TACTAAAGTT
* *
918636 AATTAAATAAA-ATAATTAGTCTAGGGACTA
1 AATTAAAAAAACAT-ATAAGTCTAGGGACTA
*
918666 AATTAAAAAAACATATAAGTCTAGGGACTC
1 AATTAAAAAAACATATAAGTCTAGGGACTA
918696 AATT
1 AATT
918700 GAAACTAACC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 28 0.93
31 2 0.07
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.28
Consensus pattern (30 bp):
AATTAAAAAAACATATAAGTCTAGGGACTA
Found at i:948018 original size:21 final size:20
Alignment explanation
Indices: 947991--948089 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
947981 AATCAGTTTC
947991 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
948012 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
948033 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
948053 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
948074 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
948090 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 16 0.26
21 45 0.74
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:948118 original size:20 final size:20
Alignment explanation
Indices: 948056--948249 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
948046 CGATTTTCCA
* ** *
948056 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
948076 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
948096 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
948116 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
948136 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
948156 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
948176 ATATCGCAACGCGTATCGGT
1 AAATCGCAACGCGTATCCGT
* * *
948196 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
948216 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
948237 AAATCGCAACGCG
1 AAATCGCAACGCG
948250 ATATTTAAAG
Statistics
Matches: 144, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 124 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:948140 original size:60 final size:60
Alignment explanation
Indices: 948056--948249 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
948046 CGATTTTCCA
* ** * *
948056 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
948116 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * **
948176 ATATCGCAACGCGTATCGGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
948237 AAATCGCAACGCG
1 AAATCGCAACGCG
948250 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 22, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:948671 original size:33 final size:33
Alignment explanation
Indices: 948632--948702 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
948622 TTCACTTAGA
*
948632 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
948665 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
948698 TTTCA
1 TTTCA
948703 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:948839 original size:41 final size:41
Alignment explanation
Indices: 948781--948858 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
948771 TTGCAGAAGA
*
948781 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
948822 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
948859 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:948855 original size:21 final size:21
Alignment explanation
Indices: 948782--948857 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
948772 TGCAGAAGAG
*
948782 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
***
948803 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
948823 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
948844 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
948858 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.46, C:0.17, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:948861 original size:14 final size:14
Alignment explanation
Indices: 948842--948898 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
948832 GAGAAATGAA
948842 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
948856 AATCGCAACGCGATATGAA
1 AATCGCAA--CG--A-GAG
948875 AATCGCAACGAGAG
1 AATCGCAACGAGAG
948889 AATCGCAACG
1 AATCGCAACG
948899 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:948877 original size:33 final size:33
Alignment explanation
Indices: 948837--948901 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
948827 AACGAGAGAA
948837 ATGAAAATCGCAACGAGAGAATCGCAACGCGAT
1 ATGAAAATCGCAACGAGAGAATCGCAACGCGAT
948870 ATGAAAATCGCAACGAGAGAATCGCAACGCGA
1 ATGAAAATCGCAACGAGAGAATCGCAACGCGA
948902 AACCAAAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.11
Consensus pattern (33 bp):
ATGAAAATCGCAACGAGAGAATCGCAACGCGAT
Found at i:948910 original size:33 final size:33
Alignment explanation
Indices: 948840--948914 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
948830 GAGAGAAATG
* **
948840 AAAATCGCAACGAGAGAATCGCAACGCGATATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
948873 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
948906 AAAATCGCA
1 AAAATCGCA
948915 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.45, C:0.24, G:0.21, T:0.09
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:948932 original size:19 final size:19
Alignment explanation
Indices: 948910--949007 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
948900 GAAACCAAAA
*
948910 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
948929 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
948943 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
948962 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
948976 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
948995 TCGCGTTGCGATT
1 TCGCGTTGCGATT
949008 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:948951 original size:14 final size:14
Alignment explanation
Indices: 948932--949021 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
948922 TTTCATTTCG
948932 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
948946 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
948965 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
948979 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
948998 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
949012 CGTTGCGATT
1 CGTTGCGATT
949022 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:948957 original size:33 final size:33
Alignment explanation
Indices: 948915--949029 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
948905 CAAAATCGCA
948915 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
948948 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
948981 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
949014 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
949030 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:950886 original size:93 final size:93
Alignment explanation
Indices: 950727--951195 Score: 913
Period size: 93 Copynumber: 5.1 Consensus size: 93
950717 TAGATTGCTT
*
950727 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
950792 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
950820 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
950885 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
950913 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
950978 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
951006 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
951071 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
951099 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
951164 TTTGTCTTTTTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
951191 AGTAA
1 AGTAA
951196 TGCAATCCAT
Statistics
Matches: 374, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 6 0.02
93 368 0.98
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:951283 original size:19 final size:19
Alignment explanation
Indices: 951243--951371 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
951233 TAGTTTACTT
* *
951243 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
951263 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
951282 TCGCAACGCGAAATAAAAA
1 TCGCAACGCGAAACCAAAA
*
951301 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
951315 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
951334 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
951348 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
951367 TCGCA
1 TCGCA
951372 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:951317 original size:33 final size:32
Alignment explanation
Indices: 951279--951371 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
951269 CGCGAAACCA
**
951279 AAATCGCAACGCGAAATAAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
951311 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
951344 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
951372 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:951369 original size:52 final size:52
Alignment explanation
Indices: 951243--951371 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 52
951233 TAGTTTACTT
* **
951243 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACGCGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
*** *
951295 TAAAAATCGC--AACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAA-CGCGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
951348 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACGCGAAACACAAAATCGCA
951372 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
51 3 0.05
52 47 0.78
53 7 0.12
54 3 0.05
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (52 bp):
TCGCAACGCGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:951389 original size:19 final size:19
Alignment explanation
Indices: 951367--951501 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
951357 GAAACCAAAA
*
951367 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
951386 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
951402 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
951419 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
951435 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* **
951452 TTGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
951471 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
951491 TCGTGTTGCGA
1 TCGCGTTGCGA
951502 AAGTAAACTA
Statistics
Matches: 94, Mismatches: 11, Indels: 21
0.75 0.09 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 45 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:951408 original size:14 final size:14
Alignment explanation
Indices: 951389--951445 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
951379 TTTCATTTCG
951389 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
951403 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
951420 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
951436 CGTTGCGATT
1 CGTTGCGATT
951446 TTCATTTTGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:951414 original size:33 final size:33
Alignment explanation
Indices: 951372--951464 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
951362 CAAAATCGCA
*
951372 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
951405 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
951438 TTGCGATTTTCATTTTGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
951465 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:953445 original size:14 final size:14
Alignment explanation
Indices: 953426--953461 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
953416 ATTGTTTAAT
953426 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
953440 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
953454 TGATTTGT
1 TGATTTGT
953462 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:953583 original size:19 final size:19
Alignment explanation
Indices: 953567--953664 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
953557 CAAAATGACT
953567 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
953586 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
953605 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
953619 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
953638 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
953658 ATCGCAA
1 ATCGCAA
953665 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:953696 original size:53 final size:53
Alignment explanation
Indices: 953567--953680 Score: 221
Period size: 53 Copynumber: 2.2 Consensus size: 53
953557 CAAAATGACT
953567 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
953619 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
953672 ATCGCAATG
1 ATCGCAATG
953681 TGTTTATAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.48
53 32 0.52
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:953734 original size:19 final size:19
Alignment explanation
Indices: 953710--953978 Score: 291
Period size: 19 Copynumber: 15.4 Consensus size: 19
953700 CGATCTCTCG
953710 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
953729 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
953748 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
953762 TTGCAATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
953781 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
953800 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
953814 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
953833 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
953852 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
953866 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
953885 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
953904 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
953918 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
953938 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
953952 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
953971 TTGCGATT
1 TTGCGATT
953979 GTAATTTCCG
Statistics
Matches: 212, Mismatches: 12, Indels: 52
0.77 0.04 0.19
Matches are distributed among these distances:
14 34 0.16
16 30 0.14
17 27 0.13
18 3 0.01
19 106 0.50
20 12 0.06
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:953775 original size:52 final size:52
Alignment explanation
Indices: 953689--953950 Score: 499
Period size: 52 Copynumber: 5.0 Consensus size: 52
953679 TGTGTTTATA
953689 ATTTCGCATTGCGA-TCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
953740 ATTTCGCATTGCGATTCTCTCGTTGCAATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
953792 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
953844 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
953896 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
953949 AT
1 AT
953951 GTTGGGATTT
Statistics
Matches: 207, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
51 14 0.07
52 176 0.85
53 17 0.08
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:953776 original size:33 final size:33
Alignment explanation
Indices: 953729--953892 Score: 172
Period size: 33 Copynumber: 4.8 Consensus size: 33
953719 TCATTTCGCA
953729 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* *
953762 TTGCAATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
953798 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
953833 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
953866 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
953893 TTCATTTCGC
Statistics
Matches: 106, Mismatches: 14, Indels: 22
0.75 0.10 0.15
Matches are distributed among these distances:
31 9 0.08
32 5 0.05
33 62 0.58
35 5 0.05
36 4 0.04
37 2 0.02
38 7 0.07
39 3 0.03
40 9 0.08
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:956278 original size:12 final size:12
Alignment explanation
Indices: 956261--956285 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
956251 TCTTCGGGGA
956261 CTTTTTCTTCTT
1 CTTTTTCTTCTT
956273 CTTTTTCTTCTT
1 CTTTTTCTTCTT
956285 C
1 C
956286 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:956494 original size:24 final size:24
Alignment explanation
Indices: 956460--956506 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
956450 CTGAAACATC
956460 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
956484 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
956507 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:957217 original size:20 final size:20
Alignment explanation
Indices: 957189--957418 Score: 219
Period size: 20 Copynumber: 11.5 Consensus size: 20
957179 AAATTTCAGT
* * *
957189 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
957209 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
957229 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
* **
957249 GTTGCGATTTACAGATTATC
1 GTTGCGATTTACGGATTCGC
*
957269 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
957289 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
957309 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
957329 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
957349 GTTGCGATTTACGGATACGA
1 GTTGCGATTTACGGATTCGC
*
957369 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
957389 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
957409 GTTGCGATTT
1 GTTGCGATTT
957419 TGGAAAATCG
Statistics
Matches: 180, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 179 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:957435 original size:21 final size:21
Alignment explanation
Indices: 957405--957487 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
957395 ATTTTCATAT
*
957405 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
957426 TCGCAATGCGAATTTGTATTA
1 TCGCATTGCGATTTTGGAAAA
*
957447 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
957468 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
957488 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:957478 original size:42 final size:43
Alignment explanation
Indices: 957385--957483 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
957375 ATTTATGTGT
* *
957385 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
957426 TCGCAATGCGAATTTGT-AT-TATCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCATAT-TCGCATTGCGATTTTGCAA-AA
*
957468 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
957484 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 11 0.23
42 35 0.74
43 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.38
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:966244 original size:39 final size:39
Alignment explanation
Indices: 966177--966292 Score: 178
Period size: 39 Copynumber: 2.9 Consensus size: 39
966167 AGGTAATTAA
* * * *
966177 CGACGTTTATAAAAAAACTGCAACAGAGCTTGACCTTTTG
1 CGACGTTTGTAAAAAAAC-ACTATAGAGCTTGACCTTTTG
966217 CGACGTTTGTAAAAAAACACTATAGAGCTTGACCTTTTG
1 CGACGTTTGTAAAAAAACACTATAGAGCTTGACCTTTTG
*
966256 CGACGTTTGTAAAAAACCACTATAGAGCTTGACCTTT
1 CGACGTTTGTAAAAAAACACTATAGAGCTTGACCTTT
966293 CACGGCATTT
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
39 54 0.76
40 17 0.24
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (39 bp):
CGACGTTTGTAAAAAAACACTATAGAGCTTGACCTTTTG
Found at i:966308 original size:39 final size:39
Alignment explanation
Indices: 966201--966335 Score: 162
Period size: 39 Copynumber: 3.4 Consensus size: 39
966191 AAACTGCAAC
* *
966201 AGAGCTTGACCTTTTGCGACGTTTGTAAAAAAACACTAT
1 AGAGCTTGACCTTTCGCGACGTTTGTAAAAAACCACTAT
*
966240 AGAGCTTGACCTTTTGCGACGTTTGTAAAAAACCACTAT
1 AGAGCTTGACCTTTCGCGACGTTTGTAAAAAACCACTAT
* * * * *
966279 AGAGCTTGACCTTTCACGGCATTTTTAAAACAACGCCACTGT
1 AGAGCTTGACCTTTCGCGACGTTTGTAAAA-AA--CCACTAT
*
966321 AAAGCTTGACCTTTC
1 AGAGCTTGACCTTTC
966336 CCTGTGTTTA
Statistics
Matches: 85, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
39 63 0.74
40 2 0.02
42 20 0.24
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (39 bp):
AGAGCTTGACCTTTCGCGACGTTTGTAAAAAACCACTAT
Found at i:966427 original size:44 final size:44
Alignment explanation
Indices: 966283--966441 Score: 146
Period size: 44 Copynumber: 3.7 Consensus size: 44
966273 CACTATAGAG
* * * * * *
966283 CTTGACCTTTCACGGC-ATTTTTA-AAACAACGCCACTGTAAAG
1 CTTGACCTTTCACGGCGATTGTAAGAAAAAACGCCGCTATAAAT
* * * * * *
966325 CTTGACCTTTCCCTGTGTTTATAAG-AAAAACGCCGCTATAGAT
1 CTTGACCTTTCACGGCGATTGTAAGAAAAAACGCCGCTATAAAT
*
966368 CTTGATCTTTCACGGCGATTGTAAGAAAAAACGCCGCTATAAAGT
1 CTTGACCTTTCACGGCGATTGTAAGAAAAAACGCCGCTATAAA-T
* *
966413 -TTGACCTTTTACGGCGTTTGTAAGAAAAA
1 CTTGACCTTTCACGGCGATTGTAAGAAAAA
966442 TGCCACTATA
Statistics
Matches: 92, Mismatches: 21, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
42 13 0.14
43 36 0.39
44 42 0.46
45 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (44 bp):
CTTGACCTTTCACGGCGATTGTAAGAAAAAACGCCGCTATAAAT
Found at i:966437 original size:87 final size:84
Alignment explanation
Indices: 966234--966452 Score: 228
Period size: 87 Copynumber: 2.6 Consensus size: 84
966224 TGTAAAAAAA
* * *
966234 CACTATAGAGCTTGACCTTTTGCGACGTTTGT-A-AAAAA-CCACTATAGAGCTTGACCTTTCAC
1 CACTATAAAGCTTGACCTTTTACGGCGTTTGTAAGAAAAAGCCACTATAGAGCTTGACCTTTCAC
* * *
966296 GGCATTTTTAAAACAACGC
66 GGCATTGTAAAAAAAACGC
* ** * * * * * *
966315 CACTGTAAAGCTTGACCTTTCCCTGTGTTTATAAGAAAAACGCCGCTATAGATCTTGATCTTTCA
1 CACTATAAAGCTTGACCTTTTACGGCGTTTGTAAGAAAAA-GCCACTATAGAGCTTGACCTTTCA
966380 CGGCGATTGTAAGAAAAAACGC
65 CGGC-ATTGTAA-AAAAAACGC
* *
966402 CGCTATAAAGTTTGACCTTTTACGGCGTTTGTAAGAAAAATGCCACTATAG
1 CACTATAAAGCTTGACCTTTTACGGCGTTTGTAAGAAAAA-GCCACTATAG
966453 TTTAGAGCTT
Statistics
Matches: 108, Mismatches: 24, Indels: 6
0.78 0.17 0.04
Matches are distributed among these distances:
81 24 0.22
82 1 0.01
83 5 0.05
85 24 0.22
86 5 0.05
87 49 0.45
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (84 bp):
CACTATAAAGCTTGACCTTTTACGGCGTTTGTAAGAAAAAGCCACTATAGAGCTTGACCTTTCAC
GGCATTGTAAAAAAAACGC
Found at i:967538 original size:20 final size:20
Alignment explanation
Indices: 967515--967577 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
967505 TTGGTATAGG
967515 TATTAACCCTTCAGTATCGA
1 TATTAACCCTTCAGTATCGA
*
967535 TATTGACCCCTTCAGTATCGA
1 TATT-AACCCTTCAGTATCGA
* * * *
967556 TACTGACCCATGAGTATCGA
1 TATTAACCCTTCAGTATCGA
967576 TA
1 TA
967578 CATACTGATG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
20 18 0.50
21 18 0.50
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (20 bp):
TATTAACCCTTCAGTATCGA
Found at i:967547 original size:21 final size:20
Alignment explanation
Indices: 967520--967578 Score: 82
Period size: 21 Copynumber: 2.9 Consensus size: 20
967510 ATAGGTATTA
*
967520 ACCCTTCAGTATCGATATTG
1 ACCCTTCAGTATCGATACTG
967540 ACCCCTTCAGTATCGATACTG
1 A-CCCTTCAGTATCGATACTG
* *
967561 ACCCATGAGTATCGATAC
1 ACCCTTCAGTATCGATAC
967579 ATACTGATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
20 16 0.46
21 19 0.54
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (20 bp):
ACCCTTCAGTATCGATACTG
Found at i:967578 original size:20 final size:21
Alignment explanation
Indices: 967525--967578 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
967515 TATTAACCCT
* *
967525 TCAGTATCGATATTGACCCCT
1 TCAGTATCGATACTGACCCCA
967546 TCAGTATCGATACTGA-CCCA
1 TCAGTATCGATACTGACCCCA
*
967566 TGAGTATCGATAC
1 TCAGTATCGATAC
967579 ATACTGATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.30
Consensus pattern (21 bp):
TCAGTATCGATACTGACCCCA
Found at i:968644 original size:108 final size:109
Alignment explanation
Indices: 968447--968650 Score: 338
Period size: 108 Copynumber: 1.9 Consensus size: 109
968437 TAAGGGTTTA
*
968447 TTTTGAAGTTCTAAAATTGAGGATTAAGGCTCTTACCTTTGTAAAACCAGATTGGTGAAGAAAGC
1 TTTTGAAGTTCTAAAATTGAGGATTAAGGCTCTTACCTTTGTAAAACCAGATTGGTGAAGAAAGA
* * *
968512 TAATAAAGTTTCCACCTTTTTCTAATTTACCAAGGAAATGCTTG
66 TAATAAAGTTTCCACATTTCTCTAAGTTACCAAGGAAATGCTTG
* * *
968556 TTTTGAATTTCTAAAGTTGA-GATTAAGGCTCTTACCTTTGTAAAACCAGATTGGTGGAGAAAGA
1 TTTTGAAGTTCTAAAATTGAGGATTAAGGCTCTTACCTTTGTAAAACCAGATTGGTGAAGAAAGA
968620 TAATAAAGTTTCCACATTTCTCTAAGTTACC
66 TAATAAAGTTTCCACATTTCTCTAAGTTACC
968651 TAGAAAGAAT
Statistics
Matches: 88, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
108 70 0.80
109 18 0.20
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (109 bp):
TTTTGAAGTTCTAAAATTGAGGATTAAGGCTCTTACCTTTGTAAAACCAGATTGGTGAAGAAAGA
TAATAAAGTTTCCACATTTCTCTAAGTTACCAAGGAAATGCTTG
Found at i:970295 original size:23 final size:22
Alignment explanation
Indices: 970259--970304 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
970249 ATCACGTGTC
*
970259 ATAACTTACATCATGTACATATA
1 ATAACTTACATCATAT-CATATA
970282 ATAACTTATC-TCATATCATATA
1 ATAACTTA-CATCATATCATATA
970304 A
1 A
970305 CTTATGGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 13 0.62
24 1 0.05
ACGTcount: A:0.43, C:0.17, G:0.02, T:0.37
Consensus pattern (22 bp):
ATAACTTACATCATATCATATA
Found at i:995270 original size:21 final size:21
Alignment explanation
Indices: 995237--995276 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
995227 TTCTACGTGG
*
995237 TCCTTCGGGACATATATGTAA
1 TCCTTCGGAACATATATGTAA
* *
995258 TCCTTTGGAACATGTATGT
1 TCCTTCGGAACATATATGT
995277 GGTACTTCTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (21 bp):
TCCTTCGGAACATATATGTAA
Found at i:996250 original size:18 final size:18
Alignment explanation
Indices: 996229--996263 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
996219 TAATGAGAAC
*
996229 AAGATTAATAATTATAAG
1 AAGATTAATAATAATAAG
996247 AAGATTAATAATAATAA
1 AAGATTAATAATAATAA
996264 TGTAAATGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (18 bp):
AAGATTAATAATAATAAG
Found at i:1006621 original size:19 final size:17
Alignment explanation
Indices: 1006587--1006619 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1006577 TAATATATGG
1006587 TTTTTAAAAATATATAA
1 TTTTTAAAAATATATAA
*
1006604 TTTTTGAAAATATATA
1 TTTTTAAAAATATATA
1006620 TAGTATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTTTTAAAAATATATAA
Found at i:1006696 original size:20 final size:18
Alignment explanation
Indices: 1006671--1006735 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 18
1006661 ATATATATAA
*
1006671 TTTTTGAAAATATATGATTG
1 TTTTTGAAAACATAT-A-TG
1006691 TTTTTGAAAACATA-A--
1 TTTTTGAAAACATATATG
1006706 TTTTTGAAAACATATTATAG
1 TTTTTGAAAACATA-TAT-G
1006726 TTTTTGAAAA
1 TTTTTGAAAA
1006736 TATAATGTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
15 14 0.36
17 1 0.03
18 1 0.03
20 23 0.59
ACGTcount: A:0.40, C:0.03, G:0.11, T:0.46
Consensus pattern (18 bp):
TTTTTGAAAACATATATG
Found at i:1006711 original size:15 final size:15
Alignment explanation
Indices: 1006691--1006719 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1006681 TATATGATTG
1006691 TTTTTGAAAACATAA
1 TTTTTGAAAACATAA
1006706 TTTTTGAAAACATA
1 TTTTTGAAAACATA
1006720 TTATAGTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (15 bp):
TTTTTGAAAACATAA
Found at i:1006712 original size:35 final size:35
Alignment explanation
Indices: 1006667--1006741 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
1006657 AATAATATAT
* *
1006667 ATAATTTTTGAAAATATATGATTGTTTTTGAAAAC
1 ATAATTTTTGAAAACATATGATAGTTTTTGAAAAC
* *
1006702 ATAATTTTTGAAAACATATTATAGTTTTTGAAAAT
1 ATAATTTTTGAAAACATATGATAGTTTTTGAAAAC
1006737 ATAAT
1 ATAAT
1006742 GTATATTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (35 bp):
ATAATTTTTGAAAACATATGATAGTTTTTGAAAAC
Found at i:1006789 original size:2 final size:2
Alignment explanation
Indices: 1006782--1006814 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1006772 TTTATTTTAT
1006782 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1006815 TAGGTATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1007417 original size:19 final size:21
Alignment explanation
Indices: 1007376--1007417 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
1007366 TCATTTTTGT
1007376 TGTCGGAGATAAGCCAAAGGA
1 TGTCGGAGATAAGCCAAAGGA
1007397 TGTC-GAGA-AAG-CAAAGAGA
1 TGTCGGAGATAAGCCAAAG-GA
1007416 TG
1 TG
1007418 CTACCAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 5 0.25
19 7 0.35
20 4 0.20
21 4 0.20
ACGTcount: A:0.40, C:0.12, G:0.33, T:0.14
Consensus pattern (21 bp):
TGTCGGAGATAAGCCAAAGGA
Found at i:1009040 original size:18 final size:16
Alignment explanation
Indices: 1008999--1009043 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 16
1008989 GAGTAAGAAT
1008999 TTTTATTTTATTTTCA
1 TTTTATTTTATTTTCA
*
1009015 TTATTATTTTGATTTTGA
1 TT-TTATTTT-ATTTTCA
1009033 TTTCTATTTTA
1 TTT-TATTTTA
1009044 CTAACTTATC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 2 0.08
17 9 0.36
18 14 0.56
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.71
Consensus pattern (16 bp):
TTTTATTTTATTTTCA
Found at i:1014777 original size:2 final size:2
Alignment explanation
Indices: 1014772--1014806 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1014762 CCTCTCACAC
1014772 AT AT AT -T 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
1014807 CCCTCTTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1019006 original size:13 final size:13
Alignment explanation
Indices: 1018988--1019016 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1018978 TTAAATATCA
1018988 AAATAAAAAGAAG
1 AAATAAAAAGAAG
1019001 AAATAAAAAGAAG
1 AAATAAAAAGAAG
1019014 AAA
1 AAA
1019017 ATCAAGCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (13 bp):
AAATAAAAAGAAG
Found at i:1020143 original size:16 final size:17
Alignment explanation
Indices: 1020118--1020149 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1020108 TAATATATGG
1020118 TTTTTGAAAATATATAA
1 TTTTTGAAAATATATAA
1020135 TTTTT-AAAATATATA
1 TTTTTGAAAATATATA
1020150 TATATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TTTTTGAAAATATATAA
Found at i:1020148 original size:18 final size:17
Alignment explanation
Indices: 1020118--1020151 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1020108 TAATATATGG
*
1020118 TTTTTGAAAATATATAA
1 TTTTTAAAAATATATAA
1020135 TTTTTAAAATATATATA
1 TTTTTAAAA-ATATATA
1020152 TATATATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TTTTTAAAAATATATAA
Found at i:1020154 original size:24 final size:27
Alignment explanation
Indices: 1020146--1020197 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
1020136 TTTTAAAATA
1020146 TATAT-ATATATATAGTTTTGAAAACA
1 TATATAATATATATAGTTTTGAAAACA
*
1020172 TATATAATATATATGGCTTTTGAAAA
1 TATATAATATATATAG-TTTTGAAAA
1020198 TAGTTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 5 0.22
27 9 0.39
28 9 0.39
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.42
Consensus pattern (27 bp):
TATATAATATATATAGTTTTGAAAACA
Found at i:1020156 original size:26 final size:27
Alignment explanation
Indices: 1020127--1020185 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 27
1020117 GTTTTTGAAA
* *
1020127 ATATATAATTTTTAAAATATATAT-AT
1 ATATATAATTTTGAAAACATATATAAT
*
1020153 ATATATAGTTTTGAAAACATATATAAT
1 ATATATAATTTTGAAAACATATATAAT
1020180 ATATAT
1 ATATAT
1020186 GGCTTTTGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 21 0.72
27 8 0.28
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (27 bp):
ATATATAATTTTGAAAACATATATAAT
Found at i:1020174 original size:28 final size:26
Alignment explanation
Indices: 1020127--1020197 Score: 81
Period size: 28 Copynumber: 2.7 Consensus size: 26
1020117 GTTTTTGAAA
* *
1020127 ATATATAATTTT-TAAAATATATATAT
1 ATATATAGTTTTGAAAAATATATA-AT
1020153 ATATATAGTTTTGAAAACATATATAAT
1 ATATATAGTTTTGAAAA-ATATATAAT
*
1020180 ATATATGGCTTTTGAAAA
1 ATATATAG-TTTTGAAAA
1020198 TAGTTTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
26 11 0.28
27 12 0.31
28 16 0.41
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (26 bp):
ATATATAGTTTTGAAAAATATATAAT
Found at i:1020258 original size:20 final size:20
Alignment explanation
Indices: 1020227--1020291 Score: 114
Period size: 20 Copynumber: 3.3 Consensus size: 20
1020217 AAACATATAT
1020227 AATATA-TATAGTTTTTGAA
1 AATATATTATAGTTTTTGAA
1020246 AATATATTATAGTTTTTGAA
1 AATATATTATAGTTTTTGAA
*
1020266 AACATATTATAGTTTTTGAA
1 AATATATTATAGTTTTTGAA
1020286 AATATA
1 AATATA
1020292 ATGTATATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
19 6 0.14
20 37 0.86
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (20 bp):
AATATATTATAGTTTTTGAA
Found at i:1020472 original size:18 final size:18
Alignment explanation
Indices: 1020449--1020509 Score: 95
Period size: 18 Copynumber: 3.4 Consensus size: 18
1020439 GGGTATAAGG
1020449 AAGCCTGGCCCAGCTAGC
1 AAGCCTGGCCCAGCTAGC
1020467 AAGCCTGGCCCAGCTAGC
1 AAGCCTGGCCCAGCTAGC
* * *
1020485 AAACCTGGCCCAGCAATC
1 AAGCCTGGCCCAGCTAGC
1020503 AAGCCTG
1 AAGCCTG
1020510 ATAGGGGAGG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.26, C:0.38, G:0.25, T:0.11
Consensus pattern (18 bp):
AAGCCTGGCCCAGCTAGC
Done.