Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009628.1 Hibiscus syriacus cultivar Beakdansim tig00117021_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: 2284295
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 4 of 10
Found at i:789859 original size:18 final size:19
Alignment explanation
Indices: 789822--789858 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
789812 TTTTTCATTA
*
789822 TGGGGGAATCGGTTCCCCC
1 TGGGGGAATCGATTCCCCC
*
789841 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
789859 TCTAGCAGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.30, G:0.35, T:0.24
Consensus pattern (19 bp):
TGGGGGAATCGATTCCCCC
Found at i:790736 original size:18 final size:18
Alignment explanation
Indices: 790713--790749 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
790703 TGTTCTCATG
790713 CTCCTTTCTCTACTTTAT
1 CTCCTTTCTCTACTTTAT
790731 CTCCTTTCTCTACTTTAT
1 CTCCTTTCTCTACTTTAT
790749 C
1 C
790750 CCATTGCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.35, G:0.00, T:0.54
Consensus pattern (18 bp):
CTCCTTTCTCTACTTTAT
Found at i:793484 original size:30 final size:30
Alignment explanation
Indices: 793232--793473 Score: 439
Period size: 30 Copynumber: 8.1 Consensus size: 30
793222 TCCGAAGGAC
* * * *
793232 CTATCCAAAGGTCATAAAAAACCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
793262 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
793292 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
793322 CTACCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
793352 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
793382 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
793412 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
793442 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
793472 CT
1 CT
793474 GTCTATAGGT
Statistics
Matches: 206, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 206 1.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:793501 original size:30 final size:30
Alignment explanation
Indices: 793458--793551 Score: 80
Period size: 31 Copynumber: 3.1 Consensus size: 30
793448 AGAGGTCATA
* * *
793458 AAGATCCTCGGTAACTGTCTATAGGTCCCG
1 AAGAACCTAGGTAACTGTCTATATGTCCCG
* * * *
793488 AAGAACCTAGGTAAACTATCCATATGTTCCT
1 AAGAACCTAGGT-AACTGTCTATATGTCCCG
* * *
793519 TAGAACATAGGTATACTGTCTATATGTCTCG
1 AAGAACCTAGGTA-ACTGTCTATATGTCCCG
793550 AA
1 AA
793552 AGACATAGGT
Statistics
Matches: 47, Mismatches: 15, Indels: 3
0.72 0.23 0.05
Matches are distributed among these distances:
30 11 0.23
31 36 0.77
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (30 bp):
AAGAACCTAGGTAACTGTCTATATGTCCCG
Found at i:794816 original size:21 final size:21
Alignment explanation
Indices: 794779--794823 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
794769 GATTTCTGGG
*
794779 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGATACCCATT
*
794800 CAAGGGGAA-CAGATACCCCTT
1 CAAGGGGAATC-GATACCCATT
794821 CAA
1 CAA
794824 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAATCGATACCCATT
Found at i:795535 original size:22 final size:22
Alignment explanation
Indices: 795510--795560 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
795500 CACCACAGCT
*
795510 CGTATAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
*
795532 CGTAGAATTGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
795554 CGTAGAA
1 CGTAGAA
795561 TTATGTCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.18
Consensus pattern (22 bp):
CGTAGAAATGCACCGAAGTGCC
Found at i:795561 original size:22 final size:22
Alignment explanation
Indices: 795518--795562 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
795508 CTCGTATAAA
795518 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
795540 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
795562 T
1 T
795563 ATGTCCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:795822 original size:30 final size:31
Alignment explanation
Indices: 795781--795840 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
795771 TAGACATAGT
*
795781 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
795811 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
795841 AACTTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:795897 original size:29 final size:28
Alignment explanation
Indices: 795855--795925 Score: 115
Period size: 29 Copynumber: 2.5 Consensus size: 28
795845 TTTTCTGCAC
*
795855 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATA-CA
*
795884 ATTCATGTCATGTAATACATTTAATACA
1 ATTCATGTCATGTAATACATATAATACA
795912 ATTCATGTCATGTA
1 ATTCATGTCATGTA
795926 TCATAATATG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 15 0.38
29 25 0.62
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (28 bp):
ATTCATGTCATGTAATACATATAATACA
Found at i:796344 original size:67 final size:67
Alignment explanation
Indices: 796227--796377 Score: 214
Period size: 67 Copynumber: 2.2 Consensus size: 67
796217 TTTTTCTCAT
* *
796227 GGGGAATCGGTTCCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGTATCGGTT-CCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCAT-TACGA
796292 TG-A
64 TGAA
** * * *
796295 GGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCTTGCATTCTGGAAATTCATTTCGTTG
1 GGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATTACGATG
796360 AA
66 AA
796362 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
796378 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
66 5 0.07
67 59 0.79
68 11 0.15
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.28
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATTACGATG
AA
Found at i:796387 original size:21 final size:21
Alignment explanation
Indices: 796357--796399 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
796347 ATTCATTTCG
* *
796357 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
796378 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
796399 T
1 T
796400 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:802428 original size:22 final size:22
Alignment explanation
Indices: 802411--802477 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
802401 CTCGTATAAA
802411 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
802433 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
802455 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
802477 T
1 T
802478 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:802736 original size:30 final size:31
Alignment explanation
Indices: 802695--802754 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
802685 TAGACATAGT
*
802695 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
802725 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
802755 AACTTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:802811 original size:29 final size:28
Alignment explanation
Indices: 802769--802839 Score: 115
Period size: 29 Copynumber: 2.5 Consensus size: 28
802759 TTTTCTGCAC
*
802769 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATA-CA
*
802798 ATTCATGTCATGTAATACATTTAATACA
1 ATTCATGTCATGTAATACATATAATACA
802826 ATTCATGTCATGTA
1 ATTCATGTCATGTA
802840 TCATAATATG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 15 0.38
29 25 0.62
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (28 bp):
ATTCATGTCATGTAATACATATAATACA
Found at i:803300 original size:21 final size:21
Alignment explanation
Indices: 803270--803312 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
803260 ATTCATTTCG
* *
803270 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
803291 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
803312 T
1 T
803313 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:803312 original size:67 final size:67
Alignment explanation
Indices: 803141--803290 Score: 212
Period size: 67 Copynumber: 2.2 Consensus size: 67
803131 TTTTTCTCAT
* *
803141 GGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGAT
1 GGGGTATCGGTT-CCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
*
803206 GAG
65 GAA
** * * *
803209 GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTTGCATTCTGGAAATTCAT-TTCGTTG
1 GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATG
803273 AA
66 AA
803275 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
803291 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
66 22 0.30
67 41 0.55
68 11 0.15
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATG
AA
Found at i:804396 original size:13 final size:13
Alignment explanation
Indices: 804378--804404 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
804368 TAAATAAAGC
804378 TATAACACATAGG
1 TATAACACATAGG
804391 TATAACACATAGG
1 TATAACACATAGG
804404 T
1 T
804405 TGAATGATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (13 bp):
TATAACACATAGG
Found at i:804726 original size:2 final size:2
Alignment explanation
Indices: 804719--804750 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
804709 AATCTTGAGG
804719 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
804751 GAAATGAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:805542 original size:24 final size:24
Alignment explanation
Indices: 805497--805542 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
805487 ATCATTATAT
*
805497 GGCACTACGGTGCAATTCTACGGG
1 GGCACTACGGTGCAATTATACGGG
* *
805521 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
805543 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.30, T:0.26
Consensus pattern (24 bp):
GGCACTACGGTGCAATTATACGGG
Found at i:808732 original size:21 final size:21
Alignment explanation
Indices: 808706--808750 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
808696 GATTTCTGGG
* *
808706 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
808727 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
808748 CAA
1 CAA
808751 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:809591 original size:2 final size:2
Alignment explanation
Indices: 809584--809637 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
809574 AATCTTGAGG
809584 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
809626 AT AT AT AT AT AT
1 AT AT AT AT AT AT
809638 GAAATGAAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:810446 original size:23 final size:23
Alignment explanation
Indices: 810402--810446 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
810392 ATCATTATAT
*
810402 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
810425 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
810447 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:811655 original size:20 final size:20
Alignment explanation
Indices: 811630--811672 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
811620 TTTTTCATTA
*
811630 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
* *
811650 TGGGGGTATCGATTCCCCTC
1 TGGGGGAATCGATTCCCCCC
811670 TGG
1 TGG
811673 CATTCTGGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.09, C:0.30, G:0.35, T:0.26
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:813771 original size:22 final size:22
Alignment explanation
Indices: 813754--813818 Score: 114
Period size: 22 Copynumber: 3.0 Consensus size: 22
813744 CTCGTATAAA
*
813754 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
813776 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
813798 TGCACCGTAGTG-CCGTAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
813819 GATGTCCATA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
21 9 0.21
22 33 0.79
ACGTcount: A:0.25, C:0.26, G:0.28, T:0.22
Consensus pattern (22 bp):
TGCACCGTAGTGCCCGTAGAAT
Found at i:813785 original size:13 final size:13
Alignment explanation
Indices: 813767--813807 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
813757 ACCGAAGTGC
813767 CCGTAGAATTGCA
1 CCGTAGAATTGCA
813780 CCGTAG---TGC-
1 CCGTAGAATTGCA
813789 CCGTAGAATTGCA
1 CCGTAGAATTGCA
813802 CCGTAG
1 CCGTAG
813808 TGCCGTAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
9 6 0.25
10 3 0.12
12 3 0.12
13 12 0.50
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:815525 original size:21 final size:21
Alignment explanation
Indices: 815501--815545 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
815491 TCTTGTTCGT
* *
815501 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
815522 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
815543 TTG
1 TTG
815546 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:818089 original size:20 final size:20
Alignment explanation
Indices: 818064--818104 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
818054 TTTCTGGGCA
* *
818064 AGGGGAATCGGTACCCATTC
1 AGGGGAACCGATACCCATTC
*
818084 AGGGGAACCGATACCCCTTC
1 AGGGGAACCGATACCCATTC
818104 A
1 A
818105 AACGACAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.17
Consensus pattern (20 bp):
AGGGGAACCGATACCCATTC
Found at i:818998 original size:31 final size:31
Alignment explanation
Indices: 818960--819113 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
818950 AGGTCGAGGG
818960 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
818991 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
819022 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
* * *
819053 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGT
*
819084 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
819114 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGT
Found at i:822965 original size:31 final size:31
Alignment explanation
Indices: 822927--823080 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
822917 GGGTCGAGGG
822927 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
822958 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
822989 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
* * *
823020 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGT
*
823051 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
823081 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGT
Found at i:825058 original size:22 final size:22
Alignment explanation
Indices: 825041--825106 Score: 123
Period size: 22 Copynumber: 3.0 Consensus size: 22
825031 CTCGTATAAA
*
825041 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
825063 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
825085 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
825107 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.21
Consensus pattern (22 bp):
TGCACCGTAGTGCCCGTAGAAT
Found at i:825072 original size:13 final size:13
Alignment explanation
Indices: 825054--825094 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
825044 ACCGAAGTGC
825054 CCGTAGAATTGCA
1 CCGTAGAATTGCA
825067 CCGTAG---TGC-
1 CCGTAGAATTGCA
825076 CCGTAGAATTGCA
1 CCGTAGAATTGCA
825089 CCGTAG
1 CCGTAG
825095 TGCCCGTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
9 6 0.25
10 3 0.12
12 3 0.12
13 12 0.50
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:826824 original size:21 final size:21
Alignment explanation
Indices: 826800--826844 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
826790 TCTTGTTCGT
* *
826800 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
826821 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
826842 TTG
1 TTG
826845 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:829583 original size:27 final size:27
Alignment explanation
Indices: 829523--829576 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
829513 GAACTACGAA
829523 TAATTTAAGTATTATATCGGTATGTTG
1 TAATTTAAGTATTATATCGGTATGTTG
829550 TAATTTAAGTATTATATCGGTATGTTG
1 TAATTTAAGTATTATATCGGTATGTTG
829577 ATGTTTAGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.04, G:0.19, T:0.48
Consensus pattern (27 bp):
TAATTTAAGTATTATATCGGTATGTTG
Found at i:829858 original size:25 final size:26
Alignment explanation
Indices: 829824--829873 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
829814 TAAAGTTTTA
* *
829824 TTTTACTATTTTAAATACAAATTAAT
1 TTTTACTATTATAAAAACAAATTAAT
*
829850 TTTTA-TATTATAAAAATAAATTAA
1 TTTTACTATTATAAAAACAAATTAA
829874 ATAAAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (26 bp):
TTTTACTATTATAAAAACAAATTAAT
Found at i:832437 original size:123 final size:123
Alignment explanation
Indices: 832206--832437 Score: 270
Period size: 123 Copynumber: 1.9 Consensus size: 123
832196 TGGTGAAAGT
* * * *
832206 GATGAAGATGATGTTAAAGATTTGGCGTCTCCTGTAAAGTCAGGTGGAAAGAGTCTTGGTGGCAG
1 GATGAAGACGATGTTAAAGATTTGGAGTCTCCTATAAAGTCAGGTGGAAAGAGTCGTGGTGGCAG
* * *
832271 GAGTTCCACAAAAGGCCCAGCTAACGGAAGAGGCAAAGTTGGTGATATTGACCTAAGC
66 GAGTGCCACAAAAGGACCAGCTAACGGAAGAGGCAAAGGTGGTGATATTGACCTAAGC
* ** *
832329 GATGAAGACGATGTTAAAGATTTGGAGTCTTCC-ATAAAGTCGGGTGGAGGGGGTCGTGGTGGCA
1 GATGAAGACGATGTTAAAGATTTGGAGTC-TCCTATAAAGTCAGGTGGAAAGAGTCGTGGTGGCA
* ** * * **
832393 GGGGTGCGTCAACAGGATCAGCTAGTGGAAGAGG-AAGAGGTGGTG
65 GGAGTGCCACAAAAGGACCAGCTAACGGAAGAGGCAA-AGGTGGTG
832438 GACGAGGTGG
Statistics
Matches: 89, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
122 2 0.02
123 84 0.94
124 3 0.03
ACGTcount: A:0.28, C:0.13, G:0.36, T:0.22
Consensus pattern (123 bp):
GATGAAGACGATGTTAAAGATTTGGAGTCTCCTATAAAGTCAGGTGGAAAGAGTCGTGGTGGCAG
GAGTGCCACAAAAGGACCAGCTAACGGAAGAGGCAAAGGTGGTGATATTGACCTAAGC
Found at i:835336 original size:123 final size:123
Alignment explanation
Indices: 835187--835433 Score: 494
Period size: 123 Copynumber: 2.0 Consensus size: 123
835177 TTAGACAAAT
835187 AATTAATGTATTTAAATTCATACTTGGGATAATTTGGGTGAATCACTCATGTTATTTTTATTTTA
1 AATTAATGTATTTAAATTCATACTTGGGATAATTTGGGTGAATCACTCATGTTATTTTTATTTTA
835252 TATTTTATTTTATCTTTTTTCTCATTACAATGGGATTGGTCAATTTATAATTTGAAGC
66 TATTTTATTTTATCTTTTTTCTCATTACAATGGGATTGGTCAATTTATAATTTGAAGC
835310 AATTAATGTATTTAAATTCATACTTGGGATAATTTGGGTGAATCACTCATGTTATTTTTATTTTA
1 AATTAATGTATTTAAATTCATACTTGGGATAATTTGGGTGAATCACTCATGTTATTTTTATTTTA
835375 TATTTTATTTTATCTTTTTTCTCATTACAATGGGATTGGTCAATTTATAATTTGAAGC
66 TATTTTATTTTATCTTTTTTCTCATTACAATGGGATTGGTCAATTTATAATTTGAAGC
835433 A
1 A
835434 GTTTTCTATT
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
123 124 1.00
ACGTcount: A:0.29, C:0.09, G:0.13, T:0.49
Consensus pattern (123 bp):
AATTAATGTATTTAAATTCATACTTGGGATAATTTGGGTGAATCACTCATGTTATTTTTATTTTA
TATTTTATTTTATCTTTTTTCTCATTACAATGGGATTGGTCAATTTATAATTTGAAGC
Found at i:835559 original size:2 final size:2
Alignment explanation
Indices: 835552--835581 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
835542 AAAAATTGTT
835552 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
835582 CTTGTATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:858352 original size:20 final size:20
Alignment explanation
Indices: 858309--858352 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
858299 CTATAAATTT
* *
858309 TAAATTTATAAAAAAATCAT
1 TAAATTTATAAAAAAATAAG
**
858329 TAAATTTATATTAAAATAAG
1 TAAATTTATAAAAAAATAAG
858349 TAAA
1 TAAA
858353 AAAAATCAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (20 bp):
TAAATTTATAAAAAAATAAG
Found at i:866382 original size:24 final size:23
Alignment explanation
Indices: 866338--866385 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
866328 TACGGAAGAA
* *
866338 TAATTATGTTTTTTTGTTAATTT
1 TAATTATATTTTTTTGATAATTT
866361 TAATTATTATTTTTTTGATAATTT
1 TAATTA-TATTTTTTTGATAATTT
866385 T
1 T
866386 GATTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (23 bp):
TAATTATATTTTTTTGATAATTT
Found at i:867951 original size:29 final size:29
Alignment explanation
Indices: 867877--867949 Score: 130
Period size: 28 Copynumber: 2.6 Consensus size: 29
867867 ATTGTCTAGA
867877 GGGAACCGATTCCCCCTCCCCCCCCAAGG
1 GGGAACCGATTCCCCCTCCCCCCCCAAGG
867906 GGGAACCGATTCCCCCT-CCCCCCCAAGG
1 GGGAACCGATTCCCCCTCCCCCCCCAAGG
*
867934 GGGTACCGATTCCCCC
1 GGGAACCGATTCCCCC
867950 CTGATCAACG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 26 0.60
29 17 0.40
ACGTcount: A:0.16, C:0.49, G:0.22, T:0.12
Consensus pattern (29 bp):
GGGAACCGATTCCCCCTCCCCCCCCAAGG
Found at i:879904 original size:15 final size:17
Alignment explanation
Indices: 879873--879905 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
879863 ATGAATTGAT
879873 AAAATCATAGAAAATGA
1 AAAATCATAGAAAATGA
879890 AAAAT-ATAG-AAATGA
1 AAAATCATAGAAAATGA
879905 A
1 A
879906 GAAAGAACCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 4 0.25
17 5 0.31
ACGTcount: A:0.67, C:0.03, G:0.12, T:0.18
Consensus pattern (17 bp):
AAAATCATAGAAAATGA
Found at i:882484 original size:15 final size:14
Alignment explanation
Indices: 882449--882486 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
882439 AAGTTGTTAA
882449 AATTTTCAAATGGAC
1 AATTTT-AAATGGAC
882464 AA-TTTAAATGGCAC
1 AATTTTAAATGG-AC
882478 AATTTTAAA
1 AATTTTAAA
882487 GGAACATAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 6 0.29
14 7 0.33
15 8 0.38
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (14 bp):
AATTTTAAATGGAC
Found at i:887365 original size:29 final size:29
Alignment explanation
Indices: 887307--887379 Score: 112
Period size: 29 Copynumber: 2.6 Consensus size: 29
887297 TATGCCAAGC
*
887307 AAGAAAGGGACATT-ATTTTTGTGATAAT
1 AAGAAAGGGACATTAATTTTTGTGAGAAT
* *
887335 AAGAAAGTGACATTAATTTTTGTGAGGAT
1 AAGAAAGGGACATTAATTTTTGTGAGAAT
887364 AAGAAAGGGACATTAA
1 AAGAAAGGGACATTAA
887380 AATCATAAGC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 13 0.32
29 27 0.68
ACGTcount: A:0.42, C:0.04, G:0.23, T:0.30
Consensus pattern (29 bp):
AAGAAAGGGACATTAATTTTTGTGAGAAT
Found at i:889230 original size:3 final size:3
Alignment explanation
Indices: 889222--889253 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
889212 CATATCCTAT
889222 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
889254 TTATTATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:891704 original size:10 final size:10
Alignment explanation
Indices: 891689--891717 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
891679 AAAAATCTAA
891689 AATTTAAAAT
1 AATTTAAAAT
891699 AATTTAAAAT
1 AATTTAAAAT
891709 AATTTAAAA
1 AATTTAAAA
891718 ATTTTAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
AATTTAAAAT
Found at i:900107 original size:21 final size:21
Alignment explanation
Indices: 900065--900107 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
900055 TTTATGGGCT
* *
900065 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
900086 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
900107 A
1 A
900108 CGTATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:900159 original size:20 final size:20
Alignment explanation
Indices: 900134--900171 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
900124 GAATGCTAGA
*
900134 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
900154 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
900172 TATAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:900842 original size:23 final size:23
Alignment explanation
Indices: 900798--900842 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
900788 ATTATTATAT
*
900798 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
900821 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
900843 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:903242 original size:21 final size:20
Alignment explanation
Indices: 903216--903259 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
903206 GATTTCTGGG
*
903216 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGATACCC-TT
903237 CAAGGGGAATCGATACCCTT
1 CAAGGGGAATCGATACCCTT
903257 CAA
1 CAA
903260 ACGAACAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.18
Consensus pattern (20 bp):
CAAGGGGAATCGATACCCTT
Found at i:903737 original size:2 final size:2
Alignment explanation
Indices: 903730--903764 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
903720 CATGAGTTAG
903730 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 A
903765 GGAATTGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:904640 original size:32 final size:32
Alignment explanation
Indices: 904599--904695 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 32
904589 GAGTCGAGGG
904599 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
904631 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
904662 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
904694 TT
1 TT
904696 ACCGAGGATC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
31 26 0.47
32 29 0.53
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:904671 original size:31 final size:31
Alignment explanation
Indices: 904598--904698 Score: 125
Period size: 31 Copynumber: 3.2 Consensus size: 31
904588 AGAGTCGAGG
904598 GTTTACCTATGTTCT-ACGGAACATATGGACA
1 GTTTACCTATGTTCTAAC-GAACATATGGACA
**
904629 GTTTTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTCTAACGA-ACATATGGACA
* *
904661 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTAACGAACATATGGACA
904692 GTTTACC
1 GTTTACC
904699 GAGGATCTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
31 32 0.53
32 28 0.47
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTAACGAACATATGGACA
Found at i:904730 original size:30 final size:30
Alignment explanation
Indices: 904686--904779 Score: 136
Period size: 30 Copynumber: 3.1 Consensus size: 30
904676 AAGGAACATA
904686 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
904717 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * *
904747 TGGATAGTTACCG-GGGTCTGTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
904776 TGGA
1 TGGA
904780 TAGGTCCTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
29 17 0.29
30 35 0.59
31 7 0.12
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:908107 original size:21 final size:21
Alignment explanation
Indices: 908081--908125 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
908071 GATTTCTGGG
* *
908081 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
908102 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
908123 CAA
1 CAA
908126 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:908608 original size:2 final size:2
Alignment explanation
Indices: 908601--908631 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
908591 CATGAGTTAG
908601 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 A
908632 GGAATTGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:909508 original size:32 final size:32
Alignment explanation
Indices: 909467--909563 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 32
909457 GAGTCGAGGG
909467 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
909499 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
909530 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
909562 TT
1 TT
909564 ACCGAGGATC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
31 26 0.47
32 29 0.53
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:909539 original size:31 final size:31
Alignment explanation
Indices: 909466--909566 Score: 125
Period size: 31 Copynumber: 3.2 Consensus size: 31
909456 AGAGTCGAGG
909466 GTTTACCTATGTTCT-ACGGAACATATGGACA
1 GTTTACCTATGTTCTAAC-GAACATATGGACA
**
909497 GTTTTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTCTAACGA-ACATATGGACA
* *
909529 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTAACGAACATATGGACA
909560 GTTTACC
1 GTTTACC
909567 GAGGATCTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
31 32 0.53
32 28 0.47
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTAACGAACATATGGACA
Found at i:909598 original size:30 final size:30
Alignment explanation
Indices: 909554--909647 Score: 136
Period size: 30 Copynumber: 3.1 Consensus size: 30
909544 AAGGAACATA
909554 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
909585 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * *
909615 TGGATAGTTACCG-GGGTCTGTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
909644 TGGA
1 TGGA
909648 TAGGTCCTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
29 17 0.29
30 35 0.59
31 7 0.12
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:914747 original size:21 final size:21
Alignment explanation
Indices: 914705--914747 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
914695 TTTATGGGCT
* *
914705 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
914726 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
914747 A
1 A
914748 CGTATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:914799 original size:20 final size:20
Alignment explanation
Indices: 914774--914811 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
914764 GAATGCTAGA
*
914774 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
914794 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
914812 TATAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:916865 original size:23 final size:23
Alignment explanation
Indices: 916839--916889 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
916829 CAGCTCGTAT
916839 AATTGCACCGAAGTGCCACATAG
1 AATTGCACCGAAGTGCCACATAG
* * * * *
916862 AATTGTATCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACATAG
916885 AATTG
1 AATTG
916890 TATCGTAGTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACATAG
Found at i:916890 original size:23 final size:23
Alignment explanation
Indices: 916850--916902 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
916840 ATTGCACCGA
916850 AGTGCCACATAGAATTGTATCGG
1 AGTGCCACATAGAATTGTATCGG
* * *
916873 AGTGCCGCGTAGAATTGTATCGT
1 AGTGCCACATAGAATTGTATCGG
916896 AGTGCCA
1 AGTGCCA
916903 TATAATAATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (23 bp):
AGTGCCACATAGAATTGTATCGG
Found at i:917103 original size:103 final size:103
Alignment explanation
Indices: 916918--917134 Score: 321
Period size: 103 Copynumber: 2.1 Consensus size: 103
916908 TAATGTCCAT
*
916918 AAGGACCACATATCATTCCTTAAGAATCATATACATATACATATACTAGGGATCAAGTATGTGTC
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATAC----ACTAAGGATCAAGTATGTGTC
* *
916983 TCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
62 ACACCAGACTTCACACATGTTCAAAAGAATAC--ATATGTCCCG
*
917027 AAGGACCACATATCATTCCTTAAGAATCATATACATATGC-C-AAGGATCAAGTATGTGTCACAC
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACACTAAGGATCAAGTATGTGTCACAC
917090 CAGACTTCACACATGTTCAAAAGAATACATATGTCCCG
66 CAGACTTCACACATGTTCAAAAGAATACATATGTCCCG
*
917128 AATGACC
1 AAGGACC
917135 GCGTAGACCC
Statistics
Matches: 103, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
101 16 0.16
103 47 0.46
104 1 0.01
109 39 0.38
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACACTAAGGATCAAGTATGTGTCACAC
CAGACTTCACACATGTTCAAAAGAATACATATGTCCCG
Found at i:919458 original size:18 final size:18
Alignment explanation
Indices: 919435--919471 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
919425 ACTTTTTTTC
919435 GATTGACGCTTTTACAAA
1 GATTGACGCTTTTACAAA
919453 GATTGACGCTTTTACAAA
1 GATTGACGCTTTTACAAA
919471 G
1 G
919472 CTAAACGAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (18 bp):
GATTGACGCTTTTACAAA
Found at i:937479 original size:28 final size:28
Alignment explanation
Indices: 937408--937479 Score: 67
Period size: 28 Copynumber: 2.6 Consensus size: 28
937398 TTAAAGGCAC
* * *
937408 AAACCCTAAACTTTAAACCCTATATTTA
1 AAACCATAAACTCTAAACCCTAAATTTA
* *
937436 AAACCACAAAGC-CTAAAGCCTAAATTGT-
1 AAACCATAAA-CTCTAAACCCTAAATT-TA
937464 AAACCATAAACTCTAA
1 AAACCATAAACTCTAA
937480 TTCTTAAACT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
27 1 0.03
28 32 0.91
29 2 0.06
ACGTcount: A:0.47, C:0.25, G:0.04, T:0.24
Consensus pattern (28 bp):
AAACCATAAACTCTAAACCCTAAATTTA
Found at i:937523 original size:22 final size:21
Alignment explanation
Indices: 937498--937545 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
937488 CTCAAATATA
937498 AAACTATAAATCATTAAACCTT
1 AAACTATAAATCA-TAAACCTT
* *
937520 AAACCTTTAAATCATAAATCTT
1 AAA-CTATAAATCATAAACCTT
937542 AAAC
1 AAAC
937546 CCTAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 1 0.04
22 13 0.57
23 9 0.39
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (21 bp):
AAACTATAAATCATAAACCTT
Found at i:937546 original size:22 final size:23
Alignment explanation
Indices: 937504--937546 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
937494 TATAAAACTA
937504 TAAATCATTAAACCTTAAACCTT
1 TAAATCATTAAACCTTAAACCTT
*
937527 TAAATCA-TAAATCTTAAACC
1 TAAATCATTAAACCTTAAACC
937547 CTAAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.33
Consensus pattern (23 bp):
TAAATCATTAAACCTTAAACCTT
Found at i:946661 original size:16 final size:15
Alignment explanation
Indices: 946642--946671 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
946632 GAAAGAAAAG
946642 AATATTATTAATTAAT
1 AATATTATT-ATTAAT
946658 AATATTATTATTAA
1 AATATTATTATTAA
946672 ATTGGAGTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATATTATTATTAAT
Found at i:950071 original size:31 final size:31
Alignment explanation
Indices: 950033--950096 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
950023 AGGCAGCGAC
*
950033 GGTGAAA-GGAAAACTTGATTGGGTTTTGGTT
1 GGTGAAAGGGAAAA-TTGACTGGGTTTTGGTT
950064 GGTGAAAGGGAAAATTGACTGGGTTTTGGTT
1 GGTGAAAGGGAAAATTGACTGGGTTTTGGTT
950095 GG
1 GG
950097 AAATATGAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 25 0.81
32 6 0.19
ACGTcount: A:0.25, C:0.03, G:0.39, T:0.33
Consensus pattern (31 bp):
GGTGAAAGGGAAAATTGACTGGGTTTTGGTT
Found at i:963714 original size:42 final size:41
Alignment explanation
Indices: 963667--963763 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 41
963657 ATAATTTAAG
* * *
963667 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATGAAA
1 TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGAT-AAA
* * *
963709 TCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAG
1 TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGATAAA
* *
963750 TCATTCGAGCCATC
1 TCCTTCGGGCCATC
963764 CATAAAGCCT
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 13 0.28
42 33 0.72
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (41 bp):
TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGATAAA
Found at i:963942 original size:42 final size:42
Alignment explanation
Indices: 963883--964014 Score: 237
Period size: 42 Copynumber: 3.1 Consensus size: 42
963873 ACTTAGTAAG
*
963883 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAA
963925 TCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAA
* *
963967 TCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAA
964009 TCCTTC
1 TCCTTC
964015 GGGTAACTGG
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 87 1.00
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (42 bp):
TCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAA
Found at i:964074 original size:13 final size:13
Alignment explanation
Indices: 964056--964080 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
964046 TGAAGAAAAT
964056 CCATCAGTAAGTG
1 CCATCAGTAAGTG
964069 CCATCAGTAAGT
1 CCATCAGTAAGT
964081 CTTTCGAGCA
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:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:964203 original size:80 final size:80
Alignment explanation
Indices: 964070--964351 Score: 458
Period size: 80 Copynumber: 3.5 Consensus size: 80
964060 CAGTAAGTGC
964070 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
964135 GTAGTGAAGCAAATT
66 GTAGTGAAGCAAATT
* * * ** *
964150 CATCAGTAAGTCTTTCGAGCATGGTAATTAAATCCTTCGGGTAATTTTTAAGCCTTCACCGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
**
964215 GTAGTGAAGCAAACC
66 GTAGTGAAGCAAATT
964230 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
964295 GTAGTGAAGCAAATT
66 GTAGTGAAGCAAATT
* *
964310 CATCAGTAAGTCTTTCGAGCAGGATG-TTGAAATCTTTCGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGATT-AAATCCTTCGGGT
964352 CATCAGTAAG
Statistics
Matches: 183, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
79 2 0.01
80 181 0.99
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (80 bp):
CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAACTGGTAAGCCTTCACGGAAGA
GTAGTGAAGCAAATT
Found at i:964356 original size:42 final size:41
Alignment explanation
Indices: 964309--964421 Score: 147
Period size: 42 Copynumber: 2.7 Consensus size: 41
964299 TGAAGCAAAT
*
964309 TCATCAGTAAGTCTTTCGAGCAGGATGTTGAAATCTTTCGGG
1 TCATCAGTAAGTCTTTCGAGCAGGATGTT-AAATCCTTCGGG
*
964351 TCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGG
1 TCATCAGTAAGTCTTTCGAGCAGGATG-TTAAATCCTTCGGG
* * *
964393 TCATCCA-TAAGTCCTTCGGGTAGGATGTT
1 TCAT-CAGTAAGTCTTTCGAGCAGGATGTT
964422 TTCACACCAA
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
41 2 0.03
42 57 0.90
43 4 0.06
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (41 bp):
TCATCAGTAAGTCTTTCGAGCAGGATGTTAAATCCTTCGGG
Found at i:964897 original size:53 final size:53
Alignment explanation
Indices: 964834--965029 Score: 297
Period size: 53 Copynumber: 3.7 Consensus size: 53
964824 ATCAAACCAT
964834 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * *
964887 AAGATTGTTCGAGTTTTACTCCCTGAAGCAAGAGGGAGCAAACCCGTAGACAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * *
964940 AAGACTGTTTGAGTTCTACTCCTTGAAGCAAGAGGGAGCGAACCCGCT-GGTC-G
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCG-TAGG-CAG
*
964993 AAGATTGTTCGAGTTCTACTCCCTGAAGCAATAGGGA
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGA
965030 ACAAACCTTT
Statistics
Matches: 128, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
53 126 0.98
54 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (53 bp):
AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
Found at i:973622 original size:14 final size:14
Alignment explanation
Indices: 973584--973625 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
973574 CCACTAACTG
*
973584 CTTACAACATAACA
1 CTTATAACATAACA
*
973598 CTTATTACATAACA
1 CTTATAACATAACA
973612 CTTA-AACCATAACA
1 CTTATAA-CATAACA
973626 TCCTTCAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 1 0.04
14 23 0.96
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (14 bp):
CTTATAACATAACA
Found at i:981261 original size:96 final size:96
Alignment explanation
Indices: 981108--981283 Score: 307
Period size: 96 Copynumber: 1.8 Consensus size: 96
981098 TGCACTTTGT
*
981108 AGTGGAAGTTTCGATCTAACCATGGCACCCCAACCCCCGTCTCAGCCCAGGCAACCTCGAAGGTC
1 AGTGAAAGTTTCGATCTAACCATGGCACCCCAACCCCCGTCTCAGCCCAGGCAACCTCGAAGGTC
*
981173 TGTTGCAACAGACGCGGTCGTTGCATCATAC
66 TGCTGCAACAGACGCGGTCGTTGCATCATAC
* * *
981204 AGTGAAAGTTTTGATCTAACCATGGCACCCCAACCCCTGTCTCAGCCCAGGCGACCTCGAAGGTC
1 AGTGAAAGTTTCGATCTAACCATGGCACCCCAACCCCCGTCTCAGCCCAGGCAACCTCGAAGGTC
981269 TGCTGCAACAGACGC
66 TGCTGCAACAGACGC
981284 AGTGGATGCT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
96 75 1.00
ACGTcount: A:0.24, C:0.34, G:0.23, T:0.19
Consensus pattern (96 bp):
AGTGAAAGTTTCGATCTAACCATGGCACCCCAACCCCCGTCTCAGCCCAGGCAACCTCGAAGGTC
TGCTGCAACAGACGCGGTCGTTGCATCATAC
Found at i:981443 original size:129 final size:129
Alignment explanation
Indices: 981167--981457 Score: 429
Period size: 129 Copynumber: 2.3 Consensus size: 129
981157 GGCAACCTCG
* *
981167 AAGGTCTGTTGCAACAGACGCGGTCGTTGCATCATACAGTGAAAGTTTTGATCTAACCATGGCAC
1 AAGGTCTGTTGCAACAGACGCGGTCGTTGCATCATACAGTGAAAGTTTCGATCTAACCATGGCAA
* * * * *
981232 CCCAACCCCTGTCTCAGCCCAGGCGACCTCGAAGGTCTGCTGCAACAGACGCAGTGGATGCTCG
66 ACCAACCCCCGTCTCAGCCCAGGCGACCTCGAAGGTCTGCTGAAACAGACACAGTGGATGCTCA
* ** ** *
981296 AAGGTCTGCTAAAACAGACGCGGTCGTTGCATTTTGCAGTGAAAGTTTCGATCTAACCATGGCAA
1 AAGGTCTGTTGCAACAGACGCGGTCGTTGCATCATACAGTGAAAGTTTCGATCTAACCATGGCAA
*
981361 ACCAACCCCCGTCTCAGCCCAGGCGACCTCGAAGGTCTGCTGAAACAGACACGGTGGATGCTCA
66 ACCAACCCCCGTCTCAGCCCAGGCGACCTCGAAGGTCTGCTGAAACAGACACAGTGGATGCTCA
* * *
981425 AAGGTCTGTTGCATCAGACGCAGTGGTTGCATC
1 AAGGTCTGTTGCAACAGACGCGGTCGTTGCATC
981458 CTCTGCGGGT
Statistics
Matches: 141, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
129 141 1.00
ACGTcount: A:0.25, C:0.28, G:0.26, T:0.21
Consensus pattern (129 bp):
AAGGTCTGTTGCAACAGACGCGGTCGTTGCATCATACAGTGAAAGTTTCGATCTAACCATGGCAA
ACCAACCCCCGTCTCAGCCCAGGCGACCTCGAAGGTCTGCTGAAACAGACACAGTGGATGCTCA
Found at i:985439 original size:20 final size:20
Alignment explanation
Indices: 985414--985479 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
985404 GATTTCTAAA
* *
985414 TTCGCAAAGCGAATTTTGTT
1 TTCGCAAAACGAATTTTGAT
** *
985434 TTCGCAACTCG-ATTTTGAA
1 TTCGCAAAACGAATTTTGAT
*
985453 TTCGCAAAACGAATTTTAAT
1 TTCGCAAAACGAATTTTGAT
985473 TTCGCAA
1 TTCGCAA
985480 CACAAATGTT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
19 15 0.41
20 22 0.59
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36
Consensus pattern (20 bp):
TTCGCAAAACGAATTTTGAT
Found at i:985466 original size:39 final size:40
Alignment explanation
Indices: 985370--985480 Score: 134
Period size: 39 Copynumber: 2.8 Consensus size: 40
985360 AATGACCAAC
** * *
985370 AAATTCGCAACATTGAATTTTAAATTCGTAACTCGATTTCT
1 AAATTCGCAA-AACGAATTTTAATTTCGCAACTCGATTTCT
* **
985411 AAATTCGCAAAGCGAATTTTGTTTTCGCAACTCGATTT-T
1 AAATTCGCAAAACGAATTTTAATTTCGCAACTCGATTTCT
*
985450 GAATTCGCAAAACGAATTTTAATTTCGCAAC
1 AAATTCGCAAAACGAATTTTAATTTCGCAAC
985481 ACAAATGTTT
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
39 28 0.47
40 22 0.37
41 10 0.17
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (40 bp):
AAATTCGCAAAACGAATTTTAATTTCGCAACTCGATTTCT
Found at i:987895 original size:23 final size:23
Alignment explanation
Indices: 987827--987887 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
987817 TAATCTTATA
*
987827 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* * *
987850 CGGCACTTCAGTGTAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
987873 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
987888 TTTATACGAG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:989975 original size:31 final size:30
Alignment explanation
Indices: 989937--989996 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
989927 TTATATAAGC
989937 TATGTGATAAA-GTGATGGAACATGATATTTT
1 TATGTGATAAAGGT-ATGGAA-ATGATATTTT
*
989968 TATGTGATAAAGGTATGGAAATTATATTT
1 TATGTGATAAAGGTATGGAAATGATATTT
989997 CTATACAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.30
31 17 0.63
32 2 0.07
ACGTcount: A:0.37, C:0.02, G:0.22, T:0.40
Consensus pattern (30 bp):
TATGTGATAAAGGTATGGAAATGATATTTT
Found at i:990252 original size:23 final size:23
Alignment explanation
Indices: 990220--990277 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
990210 ATCTTATATA
*
990220 GCACTACGGTGCAATTCTACGCG
1 GCACTTCGGTGCAATTCTACGCG
* * *
990243 GTACTTCGGTGCAATTCTATGTG
1 GCACTTCGGTGCAATTCTACGCG
990266 GCACTTCGGTGC
1 GCACTTCGGTGC
990278 GTTTATACGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.29
Consensus pattern (23 bp):
GCACTTCGGTGCAATTCTACGCG
Found at i:991688 original size:22 final size:22
Alignment explanation
Indices: 991603--991682 Score: 92
Period size: 22 Copynumber: 3.7 Consensus size: 22
991593 TTTCTGGGAT
* *
991603 AGGGGAATTGGTACCCATT-TA
1 AGGGGAATCGGTACCCATTCAA
*
991624 A-TGGAATCGGTACCCATTCAA
1 AGGGGAATCGGTACCCATTCAA
* *
991645 GGGGGAATCGGTACCTATTCAA
1 AGGGGAATCGGTACCCATTCAA
*
991667 AGGGGAATCGATACCC
1 AGGGGAATCGGTACCC
991683 CCTCAACGAA
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
20 15 0.31
21 2 0.04
22 31 0.65
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.23
Consensus pattern (22 bp):
AGGGGAATCGGTACCCATTCAA
Found at i:993426 original size:23 final size:24
Alignment explanation
Indices: 993381--993426 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
993371 AATCTTATAT
*
993381 GGCACTACGGTGCAAATTCTACGC
1 GGCACTACGGTGCAAATTATACGC
*
993405 GGCACTTCGGTGC-AATTATACG
1 GGCACTACGGTGCAAATTATACG
993427 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (24 bp):
GGCACTACGGTGCAAATTATACGC
Found at i:1000443 original size:23 final size:23
Alignment explanation
Indices: 1000390--1000445 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
1000380 CAATCTTATA
*
1000390 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
1000413 TGGCACTTTGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
1000436 TGGCACTTCG
1 TGGCACTTCG
1000446 ATGCGTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.18, C:0.25, G:0.27, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:1000458 original size:23 final size:23
Alignment explanation
Indices: 1000390--1000458 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
1000380 CAATCTTATA
* * *
1000390 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGATGCAATTATACG
* * *
1000413 TGGCACTTTGGTGCAATTCTACG
1 TGGCACTTCGATGCAATTATACG
**
1000436 TGGCACTTCGATGCGTTTATACG
1 TGGCACTTCGATGCAATTATACG
1000459 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (23 bp):
TGGCACTTCGATGCAATTATACG
Found at i:1005067 original size:21 final size:21
Alignment explanation
Indices: 1005041--1005085 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1005031 GATTTCTGGG
* *
1005041 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1005062 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1005083 CAA
1 CAA
1005086 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1005691 original size:18 final size:18
Alignment explanation
Indices: 1005668--1005702 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1005658 CTAGGAGATT
1005668 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
1005686 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
1005703 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:1006761 original size:149 final size:149
Alignment explanation
Indices: 1006581--1006884 Score: 581
Period size: 149 Copynumber: 2.0 Consensus size: 149
1006571 GAGTCGAGGG
1006581 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
* *
1006646 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTC
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
*
1006711 TATGGCACTACGGTGCACT
131 TATGGCACTACGGTGCAAT
1006730 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1006795 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
1006860 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1006879 TCTACG
1 TCTACG
1006885 GGGCACTTCG
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:1006907 original size:23 final size:23
Alignment explanation
Indices: 1006863--1006907 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1006853 ATCATTATAT
*
1006863 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
1006886 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
1006908 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:1009617 original size:63 final size:65
Alignment explanation
Indices: 1009478--1009640 Score: 158
Period size: 63 Copynumber: 2.6 Consensus size: 65
1009468 ATTGTTCAAG
* * *
1009478 GTGTATCGATGCACATGAAGTGCATCGATGCA-CTAATTTAAAATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCTAACTTAAAATAAAAACATCGAATGCCATCA
* * * * *
1009542 GTATATAGATGCACAAGTAGTGCATCGATGCACCT-CCTT-AAATACAAACATCGAATAG-GATT
1 GTGTATCGATGCACAAGTAGTGCATCGATGCACCTAACTTAAAATAAAAACATCGAAT-GCCA-T
*
1009604 TA
64 CA
* *
1009606 -TGTATCGATGCA-TAGATAGTGAATCGATGCACCTA
1 GTGTATCGATGCACAAG-TAGTGCATCGATGCACCTA
1009641 TCAAGGGATA
Statistics
Matches: 81, Mismatches: 13, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
62 2 0.02
63 44 0.54
64 33 0.41
65 2 0.02
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (65 bp):
GTGTATCGATGCACAAGTAGTGCATCGATGCACCTAACTTAAAATAAAAACATCGAATGCCATCA
Found at i:1010324 original size:23 final size:23
Alignment explanation
Indices: 1010271--1010331 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
1010261 CAATCTTATA
*
1010271 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
1010294 GGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
1010317 TGGCACTTCGATGCA
1 TGGCACTTCGGTGCA
1010332 TTTAACGAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.26
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:1011118 original size:24 final size:24
Alignment explanation
Indices: 1011067--1011120 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1011057 GTATTCAAAA
*
1011067 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
1011091 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
1011115 TTTGAT
1 TTTGAT
1011121 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:1013745 original size:20 final size:20
Alignment explanation
Indices: 1013691--1013747 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
1013681 TTCGCGATGA
*
1013691 GATTTTCGCGTTGCAAATTT
1 GATTTTCGCGTTGCGAATTT
* * *
1013711 AAGTTTCACGTTGCGAATTT
1 GATTTTCGCGTTGCGAATTT
1013731 GATTTTCGCGTTGCGAA
1 GATTTTCGCGTTGCGAA
1013748 AGTGTACCTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40
Consensus pattern (20 bp):
GATTTTCGCGTTGCGAATTT
Found at i:1014462 original size:27 final size:27
Alignment explanation
Indices: 1014382--1014486 Score: 81
Period size: 27 Copynumber: 3.8 Consensus size: 27
1014372 AATAAAATTT
* *
1014382 ATATTATTTAT-TAATTTGATAGAAATA
1 ATATTATTTATAT-ATTTAATATAAATA
* * *
1014409 ATATTATTAAAATA-TTAATAATGAATA
1 ATATTATTTATATATTTAAT-ATAAATA
1014436 ATATTATTTATATATTTAATATTAATATA
1 ATATTATTTATATATTTAATA-TAA-ATA
*
1014465 ATAATCTAATTATAT-TTTAATA
1 AT-AT-TATTTATATATTTAATA
1014487 AAGATATTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
26 4 0.06
27 28 0.45
28 8 0.13
29 5 0.08
30 9 0.15
31 8 0.13
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTATTTATATATTTAATATAAATA
Found at i:1014508 original size:23 final size:23
Alignment explanation
Indices: 1014482--1014526 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1014472 AATTATATTT
1014482 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
1014505 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
1014527 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:1014670 original size:20 final size:20
Alignment explanation
Indices: 1014623--1014676 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
1014613 AATAAAATTA
1014623 TAAAAATAATATTTAATAAT
1 TAAAAATAATATTTAATAAT
* *
1014643 AAATAAATAAT-TTTAATATTT
1 TAA-AAATAATATTTAATA-AT
1014664 TAAAAATAATATT
1 TAAAAATAATATT
1014677 ATTAAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAAAATAATATTTAATAAT
Found at i:1014685 original size:22 final size:25
Alignment explanation
Indices: 1014641--1014704 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 25
1014631 ATATTTAATA
1014641 ATAAATAAATAATT-TTAATATTTTA-
1 ATAAAT-AAT-ATTATTAATATTTTAG
1014666 A-AAATAATATTATTAA-ATTTTATG
1 ATAAATAATATTATTAATATTTTA-G
1014690 ATAAATAATATTATT
1 ATAAATAATATTATT
1014705 TATTGTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
22 9 0.26
23 7 0.20
24 5 0.14
25 14 0.40
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
ATAAATAATATTATTAATATTTTAG
Found at i:1015282 original size:31 final size:31
Alignment explanation
Indices: 1015244--1015318 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
1015234 GCTTATCCAA
*
1015244 GTGTCTAACGTTACAAACGTTACCATTTTAG
1 GTGTCTAACATTACAAACGTTACCATTTTAG
1015275 GTGTCTAACATTACAAACGTTACCATTTTAG
1 GTGTCTAACATTACAAACGTTACCATTTTAG
*
1015306 GTGTTTGAACATT
1 GTGTCT-AACATT
1015319 TAACGGTGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 35 0.85
32 6 0.15
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.37
Consensus pattern (31 bp):
GTGTCTAACATTACAAACGTTACCATTTTAG
Found at i:1017188 original size:18 final size:18
Alignment explanation
Indices: 1017165--1017207 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1017155 CTTTAAATTA
1017165 TTTATTTAATTA-TATTCT
1 TTTATTTAATTATTA-TCT
*
1017183 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
1017201 TTTATTT
1 TTTATTT
1017208 TAAAAATAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:1017276 original size:5 final size:5
Alignment explanation
Indices: 1017256--1017325 Score: 54
Period size: 5 Copynumber: 13.4 Consensus size: 5
1017246 CTATTATTTA
* *
1017256 TTATT TTA-- TTAAT TTATT TTATT TTATCTT TTATT TTATT TTATT ATACATT
1 TTATT TTATT TTATT TTATT TTATT TTA--TT TTATT TTATT TTATT -T-TATT
*
1017308 TTATT TTACCT TTATT TT
1 TTATT TTA-TT TTATT TT
1017326 TTTCTTTCCT
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
3 3 0.06
5 36 0.68
6 6 0.11
7 8 0.15
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (5 bp):
TTATT
Found at i:1017289 original size:12 final size:11
Alignment explanation
Indices: 1017268--1017325 Score: 66
Period size: 12 Copynumber: 5.3 Consensus size: 11
1017258 ATTTTATTAA
1017268 TTTA-TTTTAT
1 TTTACTTTTAT
1017278 TTTATCTTTTAT
1 TTTA-CTTTTAT
1017290 TTTA-TTTTAT
1 TTTACTTTTAT
*
1017300 TATACATTTTAT
1 TTTAC-TTTTAT
*
1017312 TTTACCTTTAT
1 TTTACTTTTAT
1017323 TTT
1 TTT
1017326 TTTCTTTCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
10 13 0.32
11 8 0.20
12 20 0.49
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTACTTTTAT
Found at i:1017290 original size:17 final size:17
Alignment explanation
Indices: 1017268--1017325 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
1017258 ATTTTATTAA
1017268 TTTATTTTATTTTATCT
1 TTTATTTTATTTTATCT
1017285 TTTATTTTATTTTAT-T
1 TTTATTTTATTTTATCT
** *
1017301 ATACATTTTATTTTA-CC
1 -TTTATTTTATTTTATCT
1017318 TTTATTTT
1 TTTATTTT
1017326 TTTCTTTCCT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
16 7 0.21
17 27 0.79
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTATTTTATTTTATCT
Found at i:1017440 original size:8 final size:8
Alignment explanation
Indices: 1017393--1017453 Score: 54
Period size: 8 Copynumber: 7.8 Consensus size: 8
1017383 ATTTTCCCAC
1017393 TTTTTTAT
1 TTTTTTAT
1017401 TTTGTTT-T
1 TTT-TTTAT
*
1017409 ATTTTTA-
1 TTTTTTAT
**
1017416 TTTTTTCG
1 TTTTTTAT
**
1017424 TTTAATAT
1 TTTTTTAT
1017432 TTTTTTAT
1 TTTTTTAT
1017440 TTTTTTAT
1 TTTTTTAT
1017448 TTTTTT
1 TTTTTT
1017454 CTGAAATTTA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
7 8 0.20
8 30 0.73
9 3 0.07
ACGTcount: A:0.13, C:0.02, G:0.03, T:0.82
Consensus pattern (8 bp):
TTTTTTAT
Found at i:1020640 original size:1 final size:1
Alignment explanation
Indices: 1020634--1020666 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
1020624 CACAACTTCA
*
1020634 TTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1020667 AGTGGGGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:1029828 original size:2 final size:2
Alignment explanation
Indices: 1029821--1029878 Score: 66
Period size: 2 Copynumber: 29.5 Consensus size: 2
1029811 ATAATTAAAT
* * *
1029821 TA TA TA TA TA TA TA TT TA -A AA TA CTA T- TA AA 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
1029862 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1029879 CGTAAGCTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
1 2 0.04
2 44 0.92
3 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1029859 original size:31 final size:30
Alignment explanation
Indices: 1029807--1029868 Score: 97
Period size: 33 Copynumber: 2.0 Consensus size: 30
1029797 AAAAATAAAA
1029807 TAAAATAATTAAATTATATATATATATATT
1 TAAAATAATTAAATTATATATATATATATT
1029837 TAAAATACTATTAAATATATATATATATATAT
1 TAAAATA--ATTAAAT-TATATATATATATAT
1029869 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 7 0.24
32 7 0.24
33 15 0.52
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (30 bp):
TAAAATAATTAAATTATATATATATATATT
Found at i:1030237 original size:13 final size:13
Alignment explanation
Indices: 1030221--1030246 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1030211 TTATGACCAA
1030221 CAAGGCATGTTAG
1 CAAGGCATGTTAG
1030234 CAAGGCATGTTAG
1 CAAGGCATGTTAG
1030247 AGTTAGAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (13 bp):
CAAGGCATGTTAG
Found at i:1030799 original size:3 final size:3
Alignment explanation
Indices: 1030793--1030819 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1030783 TACTATAATA
1030793 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1030820 TCAATTCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1036478 original size:61 final size:61
Alignment explanation
Indices: 1036403--1036559 Score: 180
Period size: 60 Copynumber: 2.6 Consensus size: 61
1036393 TCTATTTTAT
* *
1036403 TGAGTCTCAT-GACTATTAAAAGCTATAAAATGGTC-TCTTATATGTAGGATATTGCTTTGAC
1 TGAGTCTC-TCGACTATTAAAAGTTATAAAATGGTCATC-TATATATAGGATATTGCTTTGAC
**
1036464 TGAGTCTCTCGACTATTAAAAGTTATAAACA--GTCATCTATATATAGGATATTGCTTTGGT
1 TGAGTCTCTCGACTATTAAAAGTTATAAA-ATGGTCATCTATATATAGGATATTGCTTTGAC
* * *
1036524 TG-GGCACCTCGACTATTAAAAGTTAAAAAATGGTCA
1 TGAGTC-TCTCGACTATTAAAAGTTATAAAATGGTCA
1036560 CTCGACTATT
Statistics
Matches: 83, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
59 3 0.04
60 47 0.57
61 32 0.39
62 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (61 bp):
TGAGTCTCTCGACTATTAAAAGTTATAAAATGGTCATCTATATATAGGATATTGCTTTGAC
Found at i:1037236 original size:20 final size:20
Alignment explanation
Indices: 1037213--1037341 Score: 64
Period size: 20 Copynumber: 6.3 Consensus size: 20
1037203 GTTTCCAGAT
*
1037213 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTATGACTA
** * **
1037233 TCGCATTGCGATTTTAGAAAA
1 TCGCAACGCGATTAT-GACTA
* * *
1037254 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTATG-ACTA
* *
1037274 TCGTAACGCGATAAT-ACATAA
1 TCGCAACGCGATTATGAC-T-A
* * *
1037295 TCGTAACTCGATTCTGACTA
1 TCGCAACGCGATTATGACTA
* *
1037315 TCGCAACGCGATTCTGACTG
1 TCGCAACGCGATTATGACTA
1037335 TCGCAAC
1 TCGCAAC
1037342 ACTGAATTTC
Statistics
Matches: 85, Mismatches: 18, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
18 1 0.01
20 52 0.61
21 30 0.35
22 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGATTATGACTA
Found at i:1038210 original size:24 final size:24
Alignment explanation
Indices: 1038159--1038212 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1038149 GTATTCGAAA
*
1038159 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
1038183 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
1038207 TTTGAT
1 TTTGAT
1038213 GGTGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:1038433 original size:14 final size:14
Alignment explanation
Indices: 1038404--1038440 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1038394 AAAAGAAGAA
1038404 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
1038419 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
1038433 GAAGAAAA
1 GAAGAAAA
1038441 TGCCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:1040286 original size:18 final size:18
Alignment explanation
Indices: 1040263--1040297 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1040253 AGCAAAAGGC
*
1040263 AATCAAAATTGCAATCAA
1 AATCAAAATTACAATCAA
1040281 AATCAAAATTACAATCA
1 AATCAAAATTACAATCA
1040298 CAACCGGCTT
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:0.57, C:0.17, G:0.03, T:0.23
Consensus pattern (18 bp):
AATCAAAATTACAATCAA
Found at i:1040607 original size:140 final size:140
Alignment explanation
Indices: 1040355--1040637 Score: 539
Period size: 140 Copynumber: 2.0 Consensus size: 140
1040345 ACAAACGTTG
1040355 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGT
*
1040420 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
1040485 CGAATTTGAC
131 CGAATTTGAC
*
1040495 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGT
*
1040560 TTGAACATTGCTCTGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
1040625 CGAATTTGAC
131 CGAATTTGAC
1040635 TAT
1 TAT
1040638 CGCAACGCGA
Statistics
Matches: 140, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 140 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.43
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGT
TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:1040633 original size:20 final size:20
Alignment explanation
Indices: 1040608--1040769 Score: 161
Period size: 20 Copynumber: 8.8 Consensus size: 20
1040598 TTACACATTC
*
1040608 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1040628 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
1040648 ATATGACTATCGCAATG-TA
1 ATTTGACTATCGCAACGCGA
1040667 A----A--ATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1040681 ATTTGACTATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
1040701 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
1040721 ATATGACTATCACAACGC-A
1 ATTTGACTATCGCAACGCGA
*
1040740 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1040755 ATTTGACTATCGCAA
1 ATTTGACTATCGCAA
1040770 TGAGAAAATC
Statistics
Matches: 116, Mismatches: 13, Indels: 26
0.75 0.08 0.17
Matches are distributed among these distances:
13 8 0.07
14 11 0.09
15 4 0.03
18 1 0.01
19 5 0.04
20 87 0.75
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:1040701 original size:73 final size:74
Alignment explanation
Indices: 1040608--1040771 Score: 276
Period size: 73 Copynumber: 2.2 Consensus size: 74
1040598 TTACACATTC
* * * * *
1040608 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACGCGAATATGACTATCGCAATG-TAAAATC
1 ATTTGACTATCGCAATGCGAATTTGACTATCGCAACGCGAATATGACTATCACAACGCAAAAATC
1040672 GCAACGCGA
66 GCAACGCGA
1040681 ATTTGACTATCGCAATGCGAATTTGACTATCGCAACGCGAATATGACTATCACAACGCAAAAATC
1 ATTTGACTATCGCAATGCGAATTTGACTATCGCAACGCGAATATGACTATCACAACGCAAAAATC
1040746 GCAACGCGA
66 GCAACGCGA
1040755 ATTTGACTATCGCAATG
1 ATTTGACTATCGCAATG
1040772 AGAAAATCGC
Statistics
Matches: 85, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
73 53 0.62
74 32 0.38
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (74 bp):
ATTTGACTATCGCAATGCGAATTTGACTATCGCAACGCGAATATGACTATCACAACGCAAAAATC
GCAACGCGA
Found at i:1040728 original size:40 final size:34
Alignment explanation
Indices: 1040636--1040803 Score: 178
Period size: 34 Copynumber: 4.8 Consensus size: 34
1040626 GAATTTGACT
* *
1040636 ATCGCAACGCGAATATGACTATCGCAATG-TAAA
1 ATCGCAACGCGAATTTGACTATCGCAATGCAAAA
*
1040669 ATCGCAACGCGAATTTGACTATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAATTTGACTATCGCAATGC-AA----A-A
* * *
1040709 ATCGCAACGCGAATATGACTATCACAACGCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAATGCAAAA
1040743 ATCGCAACGCGAATTTGACTATCGCAATG-AGAAA
1 ATCGCAACGCGAATTTGACTATCGCAATGCA-AAA
* * *
1040777 ATCGCAAAGCGTATTAGACTATCGCAA
1 ATCGCAACGCGAATTTGACTATCGCAA
1040804 CGCGAATTGA
Statistics
Matches: 114, Mismatches: 13, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
33 29 0.25
34 53 0.46
35 2 0.02
39 3 0.03
40 27 0.24
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (34 bp):
ATCGCAACGCGAATTTGACTATCGCAATGCAAAA
Found at i:1040820 original size:19 final size:20
Alignment explanation
Indices: 1040669--1040820 Score: 71
Period size: 20 Copynumber: 8.2 Consensus size: 20
1040659 GCAATGTAAA
* *
1040669 ATCGCAACGCGAATTTGACT
1 ATCGCAAAGCGAATTAGACT
* *
1040689 ATCGCAATGCGAATTTGACT
1 ATCGCAAAGCGAATTAGACT
*
1040709 ATCGCAACGCGAA-TATGACT
1 ATCGCAAAGCGAATTA-GACT
* *
1040729 ATCACAACGC-AA--A-A--
1 ATCGCAAAGCGAATTAGACT
* *
1040743 ATCGCAACGCGAATTTGACT
1 ATCGCAAAGCGAATTAGACT
* *
1040763 ATCGCAATGAG-A--A-A--
1 ATCGCAAAGCGAATTAGACT
*
1040777 ATCGCAAAGCGTATTAGACT
1 ATCGCAAAGCGAATTAGACT
*
1040797 ATCGCAACGCGAATT-GACT
1 ATCGCAAAGCGAATTAGACT
*
1040816 TTCGC
1 ATCGC
1040821 GTTGCGATTT
Statistics
Matches: 105, Mismatches: 14, Indels: 27
0.72 0.10 0.18
Matches are distributed among these distances:
14 18 0.17
15 3 0.03
16 2 0.02
17 1 0.01
18 3 0.03
19 12 0.11
20 66 0.63
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAAAGCGAATTAGACT
Done.