Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001838.1 Hibiscus syriacus cultivar Beakdansim tig00003721_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: 3924084
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 18
Found at i:1078623 original size:21 final size:21
Alignment explanation
Indices: 1078599--1078663 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 21
1078589 TCATTCCTCG
1078599 AGAGTCCCCTCTCACCGTTCA
1 AGAGTCCCCTCTCACCGTTCA
* * * * *
1078620 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCTCACCGTTCA
* *
1078641 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCTCACCGTTCA
1078662 AG
1 AG
1078664 CGCCCGATTC
Statistics
Matches: 31, Mismatches: 12, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.23, C:0.35, G:0.20, T:0.22
Consensus pattern (21 bp):
AGAGTCCCCTCTCACCGTTCA
Found at i:1080034 original size:14 final size:14
Alignment explanation
Indices: 1080014--1080050 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
1080004 GATTGTTTAA
1080014 TTGATTTGTAAAA-
1 TTGATTTGTAAAAG
1080027 TATGATTTGTAAAAG
1 T-TGATTTGTAAAAG
1080042 TTGATTTGT
1 TTGATTTGT
1080051 TTAATTGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.05
14 20 0.91
15 1 0.05
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:1080173 original size:19 final size:17
Alignment explanation
Indices: 1080157--1080207 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 17
1080147 AAAAATGACT
1080157 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
1080176 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
1080190 ATCGCAATGCGAAATGA
1 ATCGCAATGCGAAATGA
1080207 A
1 A
1080208 AATCGCAACG
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.30
16 5 0.19
17 7 0.26
19 7 0.26
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.14
Consensus pattern (17 bp):
ATCGCAATGCGAAATGA
Found at i:1080199 original size:33 final size:33
Alignment explanation
Indices: 1080157--1080236 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
1080147 AAAAATGACT
* *
1080157 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1080190 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1080223 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
1080237 CTAAATTCGC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1080213 original size:19 final size:19
Alignment explanation
Indices: 1080157--1080215 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
1080147 AAAAATGACT
1080157 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1080176 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1080190 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1080209 ATCGCAA
1 ATCGCAA
1080216 CGACAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1080288 original size:33 final size:33
Alignment explanation
Indices: 1080246--1080372 Score: 200
Period size: 33 Copynumber: 3.8 Consensus size: 33
1080236 ACTAAATTCG
* *
1080246 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
1080279 CGTTGCGATTTTCATTTCGCATTACGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
1080312 CATTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* *
1080345 CGTTGTGATTTTCATTTCGCATTACGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1080373 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 86 1.00
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:1080325 original size:66 final size:66
Alignment explanation
Indices: 1080248--1080372 Score: 223
Period size: 66 Copynumber: 1.9 Consensus size: 66
1080238 TAAATTCGCG
*
1080248 TTGCGATTTTCATTTCGCTTTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTACGATTCTCTC
1 TTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTACGATTCTCTC
1080313 A
66 A
* *
1080314 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGTGATTTTCATTTCGCATTACGAT
1 TTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTACGAT
1080373 AGTAATTTCC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.46
Consensus pattern (66 bp):
TTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTACGATTCTCTC
A
Found at i:1080336 original size:19 final size:19
Alignment explanation
Indices: 1080242--1080372 Score: 76
Period size: 19 Copynumber: 7.7 Consensus size: 19
1080232 CGAAACTAAA
*
1080242 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
1080261 TTCGCTTTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
1080277 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
1080294 TTCGCATTACGA--TTC--
1 TTCGCATTGCGATTTTCAT
*
1080309 -TCTCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
1080327 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
* *
1080343 CTCG--TTGTGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
1080360 TTCGCATTACGAT
1 TTCGCATTGCGAT
1080373 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 14, Indels: 30
0.65 0.11 0.24
Matches are distributed among these distances:
14 20 0.24
16 16 0.19
17 16 0.19
19 31 0.37
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.46
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:1082702 original size:14 final size:14
Alignment explanation
Indices: 1082683--1082709 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1082673 TCCCGTGGCA
1082683 TTTTCTTTGGGGAC
1 TTTTCTTTGGGGAC
1082697 TTTTCTTTGGGGA
1 TTTTCTTTGGGGA
1082710 TTTCTTCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.11, G:0.30, T:0.52
Consensus pattern (14 bp):
TTTTCTTTGGGGAC
Found at i:1082943 original size:24 final size:24
Alignment explanation
Indices: 1082909--1082962 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1082899 CTGAAAAATC
1082909 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1082933 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1082957 ATCAAA
1 ATCAAA
1082963 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1082976 original size:24 final size:24
Alignment explanation
Indices: 1082909--1082976 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1082899 CTGAAAAATC
* * *
1082909 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
1082933 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1082957 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1082977 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1083848 original size:20 final size:21
Alignment explanation
Indices: 1083825--1083952 Score: 151
Period size: 20 Copynumber: 6.4 Consensus size: 21
1083815 AGAATCTCGT
1083825 TGCGATTTAC-TAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
1083845 TGCGA-TTACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
*
1083865 TGCGA-TTACGTAAATCGTAA
1 TGCGATTTACGTAAATCGCAA
* * *
1083885 TGCGAATTAGGAAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
*
1083906 TGCGA-TTACGTAAATCACAA
1 TGCGATTTACGTAAATCGCAA
* *
1083926 TGCGA-ATACGT-AATCGCAT
1 TGCGATTTACGTAAATCGCAA
1083945 TGCGATTT
1 TGCGATTT
1083953 TCCATTGCGA
Statistics
Matches: 94, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
19 15 0.16
20 62 0.66
21 17 0.18
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (21 bp):
TGCGATTTACGTAAATCGCAA
Found at i:1083911 original size:41 final size:41
Alignment explanation
Indices: 1083825--1083951 Score: 163
Period size: 41 Copynumber: 3.2 Consensus size: 41
1083815 AGAATCTCGT
*
1083825 TGCGATTTAC-TAAATCGCAATGCG-ATTACGTAAATCGCAA
1 TGCGA-TTACGTAAATCGCAATGCGAATTACGAAAATCGCAA
* *
1083865 TGCGATTACGTAAATCGTAATGCGAATTAGGAAAATCGCAA
1 TGCGATTACGTAAATCGCAATGCGAATTACGAAAATCGCAA
* * *
1083906 TGCGATTACGTAAATCACAATGCGAA-TACG-TAATCGCAT
1 TGCGATTACGTAAATCGCAATGCGAATTACGAAAATCGCAA
1083945 TGCGATT
1 TGCGATT
1083952 TTCCATTGCG
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
39 18 0.23
40 21 0.27
41 38 0.49
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (41 bp):
TGCGATTACGTAAATCGCAATGCGAATTACGAAAATCGCAA
Found at i:1083969 original size:33 final size:34
Alignment explanation
Indices: 1083932--1084026 Score: 120
Period size: 41 Copynumber: 2.6 Consensus size: 34
1083922 ACAATGCGAA
1083932 TACGTAATCGCATTGCGATTTTC-CATTGCGATT
1 TACGTAATCGCATTGCGATTTTCACATTGCGATT
1083965 TACGTAATCGCATTGCGATTTTCCTAATTCACATTGCGATT
1 TACGTAATCGCATTGCGA---T--T--TTCACATTGCGATT
1084006 TACGTAATCGCATTGCGATTT
1 TACGTAATCGCATTGCGATTT
1084027 AGGAAAATCG
Statistics
Matches: 54, Mismatches: 0, Indels: 15
0.78 0.00 0.22
Matches are distributed among these distances:
33 18 0.33
34 1 0.02
36 2 0.04
38 2 0.04
40 3 0.06
41 28 0.52
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (34 bp):
TACGTAATCGCATTGCGATTTTCACATTGCGATT
Found at i:1084001 original size:21 final size:20
Alignment explanation
Indices: 1083824--1084027 Score: 144
Period size: 20 Copynumber: 10.5 Consensus size: 20
1083814 TAGAATCTCG
1083824 TTGCGATTTAC-TAAATCGCA
1 TTGCGATTTACGT-AATCGCA
*
1083844 ATGCGA-TTACGTAAATCGCA
1 TTGCGATTTACGT-AATCGCA
* *
1083864 ATGCGA-TTACGTAAATCGTA
1 TTGCGATTTACGT-AATCGCA
* * * *
1083884 ATGCGAATTAGGAAAATCGCA
1 TTGCGATTTACG-TAATCGCA
* *
1083905 ATGCGA-TTACGTAAATCACA
1 TTGCGATTTACGT-AATCGCA
* *
1083925 ATGCGA-ATACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
1083944 TTGCGA-TT---T--TC-CA
1 TTGCGATTTACGTAATCGCA
1083957 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
* * *
1083977 TTGCGATTTTCCTAATTCACA
1 TTGCGATTTACGTAA-TCGCA
1083998 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
1084018 TTGCGATTTA
1 TTGCGATTTA
1084028 GGAAAATCGC
Statistics
Matches: 154, Mismatches: 18, Indels: 24
0.79 0.09 0.12
Matches are distributed among these distances:
13 8 0.05
14 4 0.03
16 1 0.01
17 1 0.01
19 18 0.12
20 89 0.58
21 33 0.21
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (20 bp):
TTGCGATTTACGTAATCGCA
Found at i:1084037 original size:21 final size:20
Alignment explanation
Indices: 1083824--1084066 Score: 139
Period size: 20 Copynumber: 12.3 Consensus size: 20
1083814 TAGAATCTCG
*
1083824 TTGCGATTTACTAAATCGCA
1 TTGCGATTTACGAAATCGCA
*
1083844 ATGCGA-TTACGTAAATCGCA
1 TTGCGATTTACG-AAATCGCA
* *
1083864 ATGCGA-TTACGTAAATCGTA
1 TTGCGATTTACG-AAATCGCA
* * *
1083884 ATGCGAATTAGGAAAATCGCA
1 TTGCGATTTACG-AAATCGCA
* *
1083905 ATGCGA-TTACGTAAATCACA
1 TTGCGATTTACG-AAATCGCA
* * *
1083925 ATGCGA-ATACGTAATCGCA
1 TTGCGATTTACGAAATCGCA
1083944 TTGCGATTT------TC-CA
1 TTGCGATTTACGAAATCGCA
*
1083957 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGAAATCGCA
* * * *
1083977 TTGCGATTTTCCTAATTCACA
1 TTGCGA-TTTACGAAATCGCA
*
1083998 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGAAATCGCA
*
1084018 TTGCGATTTAGGAAAATCGCA
1 TTGCGATTTACG-AAATCGCA
* **
1084039 ATGCGAATTTGGGAAATCGCA
1 TTGCG-ATTTACGAAATCGCA
*
1084060 ATGCGAT
1 TTGCGAT
1084067 AGTCAGAATC
Statistics
Matches: 182, Mismatches: 28, Indels: 26
0.77 0.12 0.11
Matches are distributed among these distances:
13 11 0.06
14 2 0.01
19 17 0.09
20 90 0.49
21 56 0.31
22 6 0.03
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (20 bp):
TTGCGATTTACGAAATCGCA
Found at i:1084044 original size:41 final size:41
Alignment explanation
Indices: 1083958--1084044 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
1083948 GATTTTCCAT
* * * *
1083958 TGCGATTTACGTAATCGCATTGCGATTTTCCTAATTCACAT
1 TGCGATTTACGTAATCGCATTGCGATTTACCAAAATCACAA
** *
1083999 TGCGATTTACGTAATCGCATTGCGATTTAGGAAAATCGCAA
1 TGCGATTTACGTAATCGCATTGCGATTTACCAAAATCACAA
1084040 TGCGA
1 TGCGA
1084045 ATTTGGGAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (41 bp):
TGCGATTTACGTAATCGCATTGCGATTTACCAAAATCACAA
Found at i:1084053 original size:22 final size:21
Alignment explanation
Indices: 1084011--1084065 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
1084001 CGATTTACGT
*
1084011 AATCGCATTGCG-ATTTAGGAA
1 AATCGCAATGCGAATTTAGG-A
*
1084032 AATCGCAATGCGAATTTGGGA
1 AATCGCAATGCGAATTTAGGA
1084053 AATCGCAATGCGA
1 AATCGCAATGCGA
1084066 TAGTCAGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 25 0.81
22 6 0.19
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (21 bp):
AATCGCAATGCGAATTTAGGA
Found at i:1085455 original size:27 final size:27
Alignment explanation
Indices: 1085412--1085464 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
1085402 AGATGCAAGA
* *
1085412 AAAAAATATAAAATTAAGGGATTAAAT
1 AAAAAATAGAAAATTAAAGGATTAAAT
* *
1085439 AAAAAATAGAAATTTAAAGTATTAAA
1 AAAAAATAGAAAATTAAAGGATTAAA
1085465 ATATCGAAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.26
Consensus pattern (27 bp):
AAAAAATAGAAAATTAAAGGATTAAAT
Found at i:1087271 original size:20 final size:20
Alignment explanation
Indices: 1087246--1087287 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1087236 TAAGTCGGGC
1087246 AAAGGGGTTACAAAAGTTTT
1 AAAGGGGTTACAAAAGTTTT
*
1087266 AAAGGGGTTACAAACGTTTT
1 AAAGGGGTTACAAAAGTTTT
1087286 AA
1 AA
1087288 TTTTTTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.24, T:0.29
Consensus pattern (20 bp):
AAAGGGGTTACAAAAGTTTT
Found at i:1092582 original size:29 final size:29
Alignment explanation
Indices: 1092540--1092600 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
1092530 AGTCCATTAT
* * *
1092540 TCTTTTACTCAACAGTGTTTAATCGTTCA
1 TCTTTTACTCAACAATATTTAACCGTTCA
*
1092569 TCTTTTACTCAACAATATTTAACCGTTTA
1 TCTTTTACTCAACAATATTTAACCGTTCA
1092598 TCT
1 TCT
1092601 AACTGGCATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.46
Consensus pattern (29 bp):
TCTTTTACTCAACAATATTTAACCGTTCA
Found at i:1093035 original size:47 final size:47
Alignment explanation
Indices: 1092984--1093128 Score: 229
Period size: 47 Copynumber: 3.1 Consensus size: 47
1092974 TACTCGTTAA
* * *
1092984 TTTTATTTATGGCATCCTTTCATGTCTTAATACATTC-TTTCATGCAT
1 TTTTAGTTATGGCATCCTTTCATGCCTTAATGCA-TCATTTCATGCAT
*
1093031 TTTTAGTTATGGCATCCTTTCATGCCTTAATGCACCATTTCATGCAT
1 TTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCAT
*
1093078 TTTTAGTTATGGCATCTTTTCATGCCTTAATGCATCATTTCATGCAT
1 TTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCAT
1093125 TTTT
1 TTTT
1093129 TTTTATTATG
Statistics
Matches: 91, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
46 1 0.01
47 90 0.99
ACGTcount: A:0.21, C:0.20, G:0.11, T:0.48
Consensus pattern (47 bp):
TTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCAT
Found at i:1093118 original size:20 final size:20
Alignment explanation
Indices: 1093042--1093122 Score: 63
Period size: 20 Copynumber: 3.7 Consensus size: 20
1093032 TTTAGTTATG
*
1093042 GCATCCTTTCATGCCTTAAT
1 GCATCATTTCATGCCTTAAT
* *
1093062 GCACCATTTCATGCATTTTTAGTTAT
1 GCATCATTTCATGC---CTTA---AT
*
1093088 GGCATCTTTTCATGCCTTAAT
1 -GCATCATTTCATGCCTTAAT
1093109 GCATCATTTCATGC
1 GCATCATTTCATGC
1093123 ATTTTTTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
20 25 0.53
21 2 0.04
23 3 0.06
24 3 0.06
26 2 0.04
27 12 0.26
ACGTcount: A:0.21, C:0.25, G:0.12, T:0.42
Consensus pattern (20 bp):
GCATCATTTCATGCCTTAAT
Found at i:1093199 original size:34 final size:34
Alignment explanation
Indices: 1093155--1093441 Score: 178
Period size: 34 Copynumber: 7.5 Consensus size: 34
1093145 TTTCAAGCCA
*
1093155 ATAATGCACCCATATGCATTATTCTTTTATGCTT
1 ATAATGCACCCATATGCATTATTCTTTTATGCTG
* *
1093189 ATAATACACCCATATGCATTTCGGCTATGACATCCTTTTATGCCG
1 ATAATGCACCCATATGCA--T----TAT----T-CTTTTATGCTG
1093234 ATAATGCACCCATATGCATTATTCTTTTATGCTG
1 ATAATGCACCCATATGCATTATTCTTTTATGCTG
* **
1093268 ATAATGTACCCATATGCATTTCAGCTATGACATCCTTTCATGCCA
1 ATAATGCACCCATATGCA-TT-A--T-T--C-T--TTT-ATGCTG
* *
1093313 ATAATGTACCCATATGCATTATTCTTTTATGATG
1 ATAATGCACCCATATGCATTATTCTTTTATGCTG
*
1093347 ATAATGCACCCATATGCATTTTAGCTATGGCATCCTTTCATGCTA
1 ATAATGCACCCATATGCA--TTA--T-T--C-T--TTT-ATGCTG
* *
1093392 ATAATTCACCCATATGCATTGTTCTTTTATGCTG
1 ATAATGCACCCATATGCATTATTCTTTTATGCTG
1093426 ATAATGCACCCATATG
1 ATAATGCACCCATATG
1093442 TATTTCAGCT
Statistics
Matches: 202, Mismatches: 18, Indels: 66
0.71 0.06 0.23
Matches are distributed among these distances:
34 84 0.42
35 9 0.04
36 5 0.02
37 2 0.01
38 4 0.02
39 5 0.02
40 5 0.02
41 4 0.02
42 2 0.01
43 4 0.02
44 9 0.04
45 69 0.34
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.38
Consensus pattern (34 bp):
ATAATGCACCCATATGCATTATTCTTTTATGCTG
Found at i:1093242 original size:79 final size:79
Alignment explanation
Indices: 1093135--1093500 Score: 552
Period size: 79 Copynumber: 4.6 Consensus size: 79
1093125 TTTTTTTTAT
* * * * *
1093135 TATGTCATCTTTTCAAGCCAATAATGCACCCATATGCATTATTCTTTTATGCTTATAATACACCC
1 TATGACATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCTGATAATGCACCC
*
1093200 ATATGCATTTCGGC
66 ATATGCATTTCAGC
* * *
1093214 TATGACATCCTTTTATGCCGATAATGCACCCATATGCATTATTCTTTTATGCTGATAATGTACCC
1 TATGACATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCTGATAATGCACCC
1093279 ATATGCATTTCAGC
66 ATATGCATTTCAGC
* *
1093293 TATGACATCCTTTCATGCCAATAATGTACCCATATGCATTATTCTTTTATGATGATAATGCACCC
1 TATGACATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCTGATAATGCACCC
*
1093358 ATATGCATTTTAGC
66 ATATGCATTTCAGC
* * * *
1093372 TATGGCATCCTTTCATGCTAATAATTCACCCATATGCATTGTTCTTTTATGCTGATAATGCACCC
1 TATGACATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCTGATAATGCACCC
*
1093437 ATATGTATTTCAGC
66 ATATGCATTTCAGC
* * *
1093451 TATGGCATCATTTCATGTCAATAATGCACCCATATGCATTATTCTTTTAT
1 TATGACATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTAT
1093501 TCATTCGTTC
Statistics
Matches: 259, Mismatches: 28, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
79 259 1.00
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.39
Consensus pattern (79 bp):
TATGACATCCTTTCATGCCAATAATGCACCCATATGCATTATTCTTTTATGCTGATAATGCACCC
ATATGCATTTCAGC
Found at i:1093411 original size:45 final size:44
Alignment explanation
Indices: 1093347--1093490 Score: 148
Period size: 45 Copynumber: 3.5 Consensus size: 44
1093337 TTTTATGATG
1093347 ATAATGCACCCATATGCATTTTAGCTATGGCATCCTTTCATGCTA
1 ATAATGCACCCATATGCATTTTAGCTATGGCAT-CTTTCATGCTA
* *
1093392 ATAATTCACCCATATGCA--TT-G-T-T--C-T-TTT-ATGCTG
1 ATAATGCACCCATATGCATTTTAGCTATGGCATCTTTCATGCTA
* *
1093426 ATAATGCACCCATATGTATTTCAGCTATGGCATCATTTCATG-TCA
1 ATAATGCACCCATATGCATTTTAGCTATGGCATC-TTTCATGCT-A
1093471 ATAATGCACCCATATGCATT
1 ATAATGCACCCATATGCATT
1093491 ATTCTTTTAT
Statistics
Matches: 80, Mismatches: 7, Indels: 24
0.72 0.06 0.22
Matches are distributed among these distances:
34 21 0.26
35 3 0.04
36 1 0.01
37 2 0.03
38 2 0.03
39 1 0.01
40 1 0.01
41 2 0.03
42 2 0.03
43 2 0.03
44 4 0.05
45 39 0.49
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (44 bp):
ATAATGCACCCATATGCATTTTAGCTATGGCATCTTTCATGCTA
Found at i:1094021 original size:17 final size:19
Alignment explanation
Indices: 1093979--1094015 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1093969 AGGTTTGATG
1093979 TTACC-TGGTATCGATACCC
1 TTACCATGGTATCGATA-CC
1093998 TTACCATGGTATCGATAC
1 TTACCATGGTATCGATAC
1094016 TACCATACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.32
Consensus pattern (19 bp):
TTACCATGGTATCGATACC
Found at i:1094057 original size:95 final size:95
Alignment explanation
Indices: 1093891--1094114 Score: 292
Period size: 95 Copynumber: 2.4 Consensus size: 95
1093881 AAGCTCAATA
* * * * * *
1093891 GTATCGATACTAC-TACCCTGGTACCGATACTTCTATACTATGGTATTGATACCCCCTTCCGGTA
1 GTATCGATAC-CCTTACCATGGTATCGATACTACCATACTATGGTAATGATACCCCCTTCCGGTA
* * *
1093955 TCAATACCAATTTTAG-GTTTGATGTTACCTG
65 TCAATACCAATTTTAGCG-TCGACGATACCTG
*
1093986 GTATCGATACCCTTACCATGGTATCGATACTACCATACTATGGTACAT-ATACCCCCTTCTGGTA
1 GTATCGATACCCTTACCATGGTATCGATACTACCATACTATGGTA-ATGATACCCCCTTCCGGTA
* *
1094050 TCGATACCAATTTTAGCGTCGACGATACTTG
65 TCAATACCAATTTTAGCGTCGACGATACCTG
1094081 GTATCGATACCCTTACCATGGTATCGATACTACC
1 GTATCGATACCCTTACCATGGTATCGATACTACC
1094115 TTTTTGATAT
Statistics
Matches: 114, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
94 1 0.01
95 111 0.97
96 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (95 bp):
GTATCGATACCCTTACCATGGTATCGATACTACCATACTATGGTAATGATACCCCCTTCCGGTAT
CAATACCAATTTTAGCGTCGACGATACCTG
Found at i:1094155 original size:21 final size:21
Alignment explanation
Indices: 1094126--1094166 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1094116 TTTTGATATC
1094126 GATACTGATTGAATCAGTATT
1 GATACTGATTGAATCAGTATT
* *
1094147 GATATTGATTGAATCTGTAT
1 GATACTGATTGAATCAGTAT
1094167 CAATACTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.41
Consensus pattern (21 bp):
GATACTGATTGAATCAGTATT
Found at i:1095281 original size:20 final size:19
Alignment explanation
Indices: 1095253--1095290 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1095243 TCATTGACCA
*
1095253 TTGACTTTGATTGTTGACT
1 TTGACTTTGATCGTTGACT
1095272 TTGACTTTTGATCGTTGAC
1 TTGAC-TTTGATCGTTGAC
1095291 CTTTTTTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.16, C:0.13, G:0.21, T:0.50
Consensus pattern (19 bp):
TTGACTTTGATCGTTGACT
Found at i:1097147 original size:9 final size:9
Alignment explanation
Indices: 1097133--1097157 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1097123 TATATACGTT
1097133 TTATTATCA
1 TTATTATCA
1097142 TTATTATCA
1 TTATTATCA
1097151 TTATTAT
1 TTATTAT
1097158 TGTTATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (9 bp):
TTATTATCA
Found at i:1101975 original size:22 final size:22
Alignment explanation
Indices: 1101947--1101996 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
1101937 TGCTCATGAT
*
1101947 TGTTTTGTTCATTGTTTAAATA
1 TGTTTTGTTCATTGTATAAATA
1101969 TGTTTTGTTCATTGTATAAATA
1 TGTTTTGTTCATTGTATAAATA
*
1101991 TTTTTT
1 TGTTTT
1101997 TCCTTGACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.22, C:0.04, G:0.12, T:0.62
Consensus pattern (22 bp):
TGTTTTGTTCATTGTATAAATA
Found at i:1112753 original size:21 final size:21
Alignment explanation
Indices: 1112727--1112780 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
1112717 AGGCACCAAG
*
1112727 GACATGAAGACTCTTCACAAA
1 GACATGAAGACCCTTCACAAA
1112748 GACATGAAGACCCTTCACAAA
1 GACATGAAGACCCTTCACAAA
1112769 GACATGAAGACC
1 GACATGAAGACC
1112781 ACTTTGCATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.43, C:0.26, G:0.17, T:0.15
Consensus pattern (21 bp):
GACATGAAGACCCTTCACAAA
Found at i:1117407 original size:42 final size:42
Alignment explanation
Indices: 1117306--1117422 Score: 128
Period size: 42 Copynumber: 2.8 Consensus size: 42
1117296 AGACTATTTC
* * *
1117306 CAAAATTGATAAGTTCTTCGGGCCATCAGTAATTCTTTCGAG
1 CAAAATTGATAAGTCCTTCGGGCCATCTGTAAGTCTTTCGAG
*** * * *
1117348 C-ATGGTGATTAAATCCTTCGGGTCATCTGTCAGTCTTTCGAG
1 CAAAATTGA-TAAGTCCTTCGGGCCATCTGTAAGTCTTTCGAG
*
1117390 CAAAATTGATAAGTCCTTCGGGCCATCTATAAG
1 CAAAATTGATAAGTCCTTCGGGCCATCTGTAAG
1117423 ACCTTCAGGC
Statistics
Matches: 57, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
41 4 0.07
42 49 0.86
43 4 0.07
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (42 bp):
CAAAATTGATAAGTCCTTCGGGCCATCTGTAAGTCTTTCGAG
Found at i:1117529 original size:259 final size:258
Alignment explanation
Indices: 1116799--1117575 Score: 1171
Period size: 258 Copynumber: 3.0 Consensus size: 258
1116789 TCTTACTTAG
* *
1116799 TAAGTCCTTCGGGTCATCAGTAAGTCTTTTGAGCATGATGATTAAATCCTTCGGGTCATCTGTAA
1 TAAGTTCTTCGGGTCATCAGTAATTCTTTTGAGCATGATGATTAAATCCTTCGGGTCATCTGTAA
* * * * * * *
1116864 GTCTTTCAAG-AAAGATGGTAAGTTCTTTGGGCCTTCCATAAGACCTTCAAGCAGGATGTTTTCA
66 GTCTTTCGAGCAAA-ATGATAAGTCCTTCGGGCCATCCATAAGACCTTCAGGCAAGATGTTTTCA
* * * * *
1116928 CATGAATTTTAAAAAATGAGAAAGTGATTTCCAATGTTTTTCATTCAGTGTTTTCAGAAAATAAA
130 CATGAATTTTAAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTCAGTGTTTTCAAAAAATGAA
*
1116993 ATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTTGACTATTTCCAAAATTGA
195 ATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAGACTATTTCCAAAATTGA
* * * * *
1117057 TAAGTTCTTTGAGTCATTAGTAATTCTTTTGAGCATGATGATTAAATCATTCGGGTCATTTGTAA
1 TAAGTTCTTCGGGTCATCAGTAATTCTTTTGAGCATGATGATTAAATCCTTCGGGTCATCTGTAA
* * * * *
1117122 GTCTTTCGAGCAAGATGATAAGTCCTTCAGGCCATCCATAAGACCTTCGGGTATGATGTTTTTC-
66 GTCTTTCGAGCAAAATGATAAGTCCTTCGGGCCATCCATAAGACCTTCAGGCAAGATG-TTTTCA
*
1117186 CATGAATTTTAAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTCAGTGTTTTCATAAAATGAA
130 CATGAATTTTAAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTCAGTGTTTTCAAAAAATGAA
*
1117251 ATTTTTGAAAAGTAAGAAAGTTATTTCCAAAGTTTCTTACCCAGTAGACTATTTCCAAAATTGA
195 ATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAGACTATTTCCAAAATTGA
* * * *
1117315 TAAGTTCTTCGGGCCATCAGTAATTCTTTCGAGCATGGTGATTAAATCCTTCGGGTCATCTGTCA
1 TAAGTTCTTCGGGTCATCAGTAATTCTTTTGAGCATGATGATTAAATCCTTCGGGTCATCTGTAA
*
1117380 GTCTTTCGAGCAAAATTGATAAGTCCTTCGGGCCATCTATAAGACCTTCAGGCAAGATGTTTTCA
66 GTCTTTCGAGCAAAA-TGATAAGTCCTTCGGGCCATCCATAAGACCTTCAGGCAAGATGTTTTCA
* * *
1117445 CATGATTTTTGAAAAATGAGAAAGCAATTTCCAAAGTTTCTCATTCAGTGTTTTCAAAAAATGAA
130 CATGAATTTTAAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTCAGTGTTTTCAAAAAATGAA
* * *
1117510 ATTTTTGAAAAGTAAGAAAGTGATTTCCAAAATTTTTTACCCAATAGACTATTTCCAAAATTGA
195 ATTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAGACTATTTCCAAAATTGA
1117574 TA
1 TA
1117576 GCATGATGAT
Statistics
Matches: 467, Mismatches: 48, Indels: 7
0.89 0.09 0.01
Matches are distributed among these distances:
258 299 0.64
259 168 0.36
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (258 bp):
TAAGTTCTTCGGGTCATCAGTAATTCTTTTGAGCATGATGATTAAATCCTTCGGGTCATCTGTAA
GTCTTTCGAGCAAAATGATAAGTCCTTCGGGCCATCCATAAGACCTTCAGGCAAGATGTTTTCAC
ATGAATTTTAAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTCAGTGTTTTCAAAAAATGAAA
TTTTTGAAAAGTAAGAAAGTGATTTCCAAAGTTTCTTACCCAGTAGACTATTTCCAAAATTGA
Found at i:1118075 original size:45 final size:44
Alignment explanation
Indices: 1118009--1118632 Score: 410
Period size: 45 Copynumber: 14.1 Consensus size: 44
1117999 TTTGGTATTG
* *
1118009 TTCTTGACTTTCTCATGAAGAGAAGTCAA-CATTTTAGTGATGTTA
1 TTCTTGACTTTCTCGTGAAGAGAAGTCAATC-TTTTAGT-ATGTCA
* * *
1118054 TTCTTGACTTTCTCGTTAAGAGAAGTCAATCTCTCAGTATTGTCA
1 TTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTTAGTA-TGTCA
* * * * * *
1118099 TTCTCGACTTTCTCGTAAAGAGGAGTTAATCTCTCAGTATTGTCA
1 TTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTTAGTA-TGTCA
* * * *
1118144 TTATTGACTTTCTCATGAAGAGGAGTCAATATTTTAGTATTGTCA
1 TTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTTAGTA-TGTCA
* *
1118189 -ACTTGACTTTCTCGT-----GAAG---ATCTTTTAGTGTTGTC-
1 TTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTTAGT-ATGTCA
*** * * * *
1118224 TTCCTTGACTTTCTCACAAAGAGGAGCCAATCTTTTAGTGTTTTC-
1 TT-CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTTAGT-ATGTCA
* * * *
1118269 TATCTTGACTTTCTCGTTAAGAGAAGTCAATCTCTCAATATTGTCA
1 T-TCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTTAGTA-TGTCA
* * *
1118315 TTCTTGAATTTCTCGTGAAGATG-AGTCAATCTCTCAGTATTGTCA
1 TTCTTGACTTTCTCGTGAAGA-GAAGTCAATCTTTTAGTA-TGTCA
* *
1118360 TTCTTGACTTTTTCGTGAAGATG-AGTCAATCTTTTAGTATTTTCA
1 TTCTTGACTTTCTCGTGAAGA-GAAGTCAATCTTTTAGTA-TGTCA
* * *
1118405 -ACTTGACTTTCTCGTGAAGATG-AGTCAATCTTTTAGTGTTATC-
1 TTCTTGACTTTCTCGTGAAGA-GAAGTCAATCTTTTAGT-ATGTCA
*** * *
1118448 TTCCTTGACTTTCTCACAAAGAGGAGTCAATCTTTTAGTGTTGTC-
1 TT-CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTTAGT-ATGTCA
* * * * *
1118493 TTCCTTGACTTTCTCGTAAAGAGGAGTCAATATTTCAATATTGTCA
1 TT-CTTGACTTTCTCGTGAAGAGAAGTCAATCTTTTAGTA-TGTCA
* *
1118539 TTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCATTGT-TGTGA
1 TTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTT--TAGTATGTCA
* *
1118584 TTCATGACTTTCTC-AGAA-AGATGAGTCAA-CATTTTAGTGATGTCA
1 TTCTTGACTTTCTCGTGAAGAGA--AGTCAATC-TTTTAGT-ATGTCA
1118629 TTCT
1 TTCT
1118633 CAACTTGACT
Statistics
Matches: 476, Mismatches: 73, Indels: 60
0.78 0.12 0.10
Matches are distributed among these distances:
36 13 0.03
37 12 0.03
39 3 0.01
42 3 0.01
43 6 0.01
44 56 0.12
45 376 0.79
46 6 0.01
47 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (44 bp):
TTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTTAGTATGTCA
Found at i:1118154 original size:90 final size:91
Alignment explanation
Indices: 1118009--1118597 Score: 500
Period size: 90 Copynumber: 6.7 Consensus size: 91
1117999 TTTGGTATTG
* * * * * *
1118009 TTCTTGACTTTCTCATGAAGAGAAGTCAA-CATTTTAGTGA-TGTTATTC-TTGACTTTCTCGTT
1 TTCTTGACTTTCTCGTAAAGAGGAGTCAATC-TTTCAGT-ATTGTCATTCATTGACTTTCTCGTG
* *
1118071 AAGAGAAGTCAATCTCTCAGTATTGTCA
64 AAGAGGAGTCAATCTTTCAGTATTGTCA
* * * *
1118099 TTCTCGACTTTCTCGTAAAGAGGAGTTAATCTCTCAGTATTGTCATT-ATTGACTTTCTCATGAA
1 TTCTTGACTTTCTCGTAAAGAGGAGTCAATCTTTCAGTATTGTCATTCATTGACTTTCTCGTGAA
* *
1118163 GAGGAGTCAATATTTTAGTATTGTCA
66 GAGGAGTCAATCTTTCAGTATTGTCA
* * * * ***
1118189 -ACTTGACTTTCTCGT---GA--AG---ATCTTTTAGTGTTGTC-TTCCTTGACTTTCTCACAAA
1 TTCTTGACTTTCTCGTAAAGAGGAGTCAATCTTTCAGTATTGTCATTCATTGACTTTCTCGTGAA
* * * *
1118244 GAGGAGCCAATCTTTTAGTGTTTTC-
66 GAGGAGTCAATCTTTCAGTATTGTCA
* * * * *
1118269 TATCTTGACTTTCTCGTTAAGAGAAGTCAATCTCTCAATATTGTCATTC-TTGAATTTCTCGTGA
1 T-TCTTGACTTTCTCGTAAAGAGGAGTCAATCTTTCAGTATTGTCATTCATTGACTTTCTCGTGA
* *
1118333 AGATGAGTCAATCTCTCAGTATTGTCA
65 AGAGGAGTCAATCTTTCAGTATTGTCA
* * * * * *
1118360 TTCTTGACTTTTTCGTGAAGATGAGTCAATCTTTTAGTATTTTCA-AC-TTGACTTTCTCGTGAA
1 TTCTTGACTTTCTCGTAAAGAGGAGTCAATCTTTCAGTATTGTCATTCATTGACTTTCTCGTGAA
* * * *
1118423 GATGAGTCAATCTTTTAGTGTTATC-
66 GAGGAGTCAATCTTTCAGTATTGTCA
** * * * *
1118448 TTCCTTGACTTTCTCACAAAGAGGAGTCAATCTTTTAGTGTTGTC-TTCCTTGACTTTCTCGTAA
1 TT-CTTGACTTTCTCGTAAAGAGGAGTCAATCTTTCAGTATTGTCATTCATTGACTTTCTCGTGA
* *
1118512 AGAGGAGTCAATATTTCAATATTGTCA
65 AGAGGAGTCAATCTTTCAGTATTGTCA
* * * * *
1118539 TTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCATTGTTGTGATTCA-TGACTTTCTC
1 TTCTTGACTTTCTCGTAAAGAGGAGTCAATCTTTCAGTATTGTCATTCATTGACTTTCTC
1118598 AGAAAGATGA
Statistics
Matches: 400, Mismatches: 78, Indels: 42
0.77 0.15 0.08
Matches are distributed among these distances:
80 2 0.00
81 48 0.12
82 14 0.04
84 2 0.00
85 2 0.00
86 2 0.00
87 2 0.00
88 2 0.00
89 87 0.22
90 229 0.57
91 10 0.03
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.41
Consensus pattern (91 bp):
TTCTTGACTTTCTCGTAAAGAGGAGTCAATCTTTCAGTATTGTCATTCATTGACTTTCTCGTGAA
GAGGAGTCAATCTTTCAGTATTGTCA
Found at i:1118388 original size:216 final size:218
Alignment explanation
Indices: 1118011--1118621 Score: 804
Period size: 216 Copynumber: 2.8 Consensus size: 218
1118001 TGGTATTGTT
** * *
1118011 CTTGACTTTCTCATGAAGAGAAGTCAA-CATTTTAGTGATGT-TATTCTTGACTTTCTCGTTAAG
1 CTTGACTTTCTCACAAAGAGGAGTCAATC-TTTTAGTGTTGTCTA-TCTTGACTTTCTCGTTAAG
* * * *
1118074 AGAAGTCAATCTCTCAGTATTGTCATTCTCGACTTTCTCGTAAAGAGGAGTTAATCTCTCAGTAT
64 AGAAGTCAATCTCTCAATATTGTCATTCTTGACTTTCTCGTGAAGA-GAGTCAATCTCTCAGTAT
* * *
1118139 TGTCATTATTGACTTTCTCATGAAGAGGAGTCAATATTTTAGTATTGTCAACTTGACTTTCTCGT
128 TGTCATTCTTGACTTTCTCGTGAAGATGAGTCAATATTTTAGTATTGTCAACTTGACTTTCTCGT
*
1118204 -GA-AG-ATCTTTTAGTGTTGTCTTC
193 AGAGAGAATCTTTTAGTGTTATCTTC
* *
1118227 CTTGACTTTCTCACAAAGAGGAGCCAATCTTTTAGTGTTTTCTATCTTGACTTTCTCGTTAAGAG
1 CTTGACTTTCTCACAAAGAGGAGTCAATCTTTTAGTGTTGTCTATCTTGACTTTCTCGTTAAGAG
*
1118292 AAGTCAATCTCTCAATATTGTCATTCTTGAATTTCTCGTGAAGATGAGTCAATCTCTCAGTATTG
66 AAGTCAATCTCTCAATATTGTCATTCTTGACTTTCTCGTGAAGA-GAGTCAATCTCTCAGTATTG
* * *
1118357 TCATTCTTGACTTTTTCGTGAAGATGAGTCAATCTTTTAGTATTTTCAACTTGACTTTCTCGTGA
130 TCATTCTTGACTTTCTCGTGAAGATGAGTCAATATTTTAGTATTGTCAACTTGACTTTCTCGT--
1118422 AGATGAGTCAATCTTTTAGTGTTATCTTC
193 AGA-GAG--AATCTTTTAGTGTTATCTTC
*
1118451 CTTGACTTTCTCACAAAGAGGAGTCAATCTTTTAGTGTTGTCT-TCCTTGACTTTCTCGTAAAGA
1 CTTGACTTTCTCACAAAGAGGAGTCAATCTTTTAGTGTTGTCTAT-CTTGACTTTCTCGTTAAGA
* * * * * *
1118515 GGAGTCAATATTTCAATATTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTTCATTGTT
65 GAAGTCAATCTCTCAATATTGTCATTCTTGACTTTCTCGTGAAGAG-AGTCAATCTCTCAGTATT
* * * *
1118580 GTGATTCATGACTTTCTCAG-AAAGATGAGTCAACATTTTAGT
129 GTCATTCTTGACTTTCTC-GTGAAGATGAGTCAATATTTTAGT
1118622 GATGTCATTC
Statistics
Matches: 347, Mismatches: 35, Indels: 18
0.87 0.09 0.05
Matches are distributed among these distances:
216 170 0.49
217 3 0.01
219 2 0.01
221 2 0.01
223 2 0.01
224 167 0.48
225 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (218 bp):
CTTGACTTTCTCACAAAGAGGAGTCAATCTTTTAGTGTTGTCTATCTTGACTTTCTCGTTAAGAG
AAGTCAATCTCTCAATATTGTCATTCTTGACTTTCTCGTGAAGAGAGTCAATCTCTCAGTATTGT
CATTCTTGACTTTCTCGTGAAGATGAGTCAATATTTTAGTATTGTCAACTTGACTTTCTCGTAGA
GAGAATCTTTTAGTGTTATCTTC
Found at i:1118646 original size:50 final size:49
Alignment explanation
Indices: 1118588--1118746 Score: 196
Period size: 51 Copynumber: 3.1 Consensus size: 49
1118578 TTGTGATTCA
* * *
1118588 TGACTTTCTCAGAAAGATGAGTCAACATTTT-AGT-GATGTCATTCTCAACT
1 TGACTTTCTC-GAGAGAGGAGTCAAC-TTTTCAGTAG-TATCATTCTCAACT
*
1118638 TGACTTTCTCGAGGAGAGGAGCCAACTTTTCAGTAGTATCATTTCTCAACT
1 TGACTTTCTCGA-GAGAGGAGTCAACTTTTCAGTAGTATCA-TTCTCAACT
*
1118689 TGACTTTCTCGCGGAGAGGAGTCAACTTTTCAGTAGTATCATTCATCAACT
1 TGACTTTCTCG-AGAGAGGAGTCAACTTTTCAGTAGTATCATTC-TCAACT
1118740 TGACTTT
1 TGACTTT
1118747 ATCATATAGA
Statistics
Matches: 97, Mismatches: 6, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
49 6 0.06
50 30 0.31
51 61 0.63
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.35
Consensus pattern (49 bp):
TGACTTTCTCGAGAGAGGAGTCAACTTTTCAGTAGTATCATTCTCAACT
Found at i:1118694 original size:51 final size:50
Alignment explanation
Indices: 1118626--1118746 Score: 206
Period size: 51 Copynumber: 2.4 Consensus size: 50
1118616 TTTAGTGATG
1118626 TCATTCTCAACTTGACTTTCTCGAGGAGAGGAGCCAACTTTTCAGTAGTA
1 TCATTCTCAACTTGACTTTCTCGAGGAGAGGAGCCAACTTTTCAGTAGTA
* *
1118676 TCATTTCTCAACTTGACTTTCTCGCGGAGAGGAGTCAACTTTTCAGTAGTA
1 TCA-TTCTCAACTTGACTTTCTCGAGGAGAGGAGCCAACTTTTCAGTAGTA
1118727 TCATTCATCAACTTGACTTT
1 TCATTC-TCAACTTGACTTT
1118747 ATCATATAGA
Statistics
Matches: 67, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
50 6 0.09
51 61 0.91
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.36
Consensus pattern (50 bp):
TCATTCTCAACTTGACTTTCTCGAGGAGAGGAGCCAACTTTTCAGTAGTA
Found at i:1118763 original size:51 final size:51
Alignment explanation
Indices: 1118629--1118769 Score: 133
Period size: 51 Copynumber: 2.7 Consensus size: 51
1118619 AGTGATGTCA
* * ** *
1118629 TTCTCAACTTGACTTTCTCGA-GGAGAGGAGCCAACTTTTCAGTAGTATCAT
1 TTCTCAACTTGACTTTATC-ACAGAGAAAAGTCAACTTTTCAGTAGTATCAT
* * * **
1118680 TTCTCAACTTGACTTTCTCGCGGAGAGGAGTCAACTTTTCAGTAGTATCA-
1 TTCTCAACTTGACTTTATCACAGAGAAAAGTCAACTTTTCAGTAGTATCAT
* *
1118730 TTCATCAACTTGACTTTATCATATAGAAAAGTCAATCTTT
1 TTC-TCAACTTGACTTTATCACAGAGAAAAGTCAA-CTTT
1118770 CTGTAATGTT
Statistics
Matches: 78, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
50 3 0.04
51 71 0.91
52 4 0.05
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (51 bp):
TTCTCAACTTGACTTTATCACAGAGAAAAGTCAACTTTTCAGTAGTATCAT
Found at i:1119837 original size:49 final size:49
Alignment explanation
Indices: 1119765--1119862 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
1119755 ACCTGAAGTT
1119765 GTAGTGGAGCGGACTTACCATTGAAAAATTGGTCGCCTTTGGATGAAAA
1 GTAGTGGAGCGGACTTACCATTGAAAAATTGGTCGCCTTTGGATGAAAA
*
1119814 GTAGTGGAGCGGACTTCCCATTGAAAAATTGGTCGCCTTTGGATGAAAA
1 GTAGTGGAGCGGACTTACCATTGAAAAATTGGTCGCCTTTGGATGAAAA
1119863 CTTGTGTCTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.27
Consensus pattern (49 bp):
GTAGTGGAGCGGACTTACCATTGAAAAATTGGTCGCCTTTGGATGAAAA
Found at i:1120013 original size:2 final size:2
Alignment explanation
Indices: 1120006--1120261 Score: 95
Period size: 2 Copynumber: 128.0 Consensus size: 2
1119996 TTATAATAAT
*
1120006 TA TA TA TA TA TA GTA -A TA TA TA GTA TA -A TA TA AA TA TA -A TA
1 TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * * * *
1120047 TA AA TA TA TA TA GTA TA TA GTT TT TA GGA GA -A 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
* * * * * *
1120089 TA TA TA TA TA TA TA TA TA TA TA GA T- TT TA GA AA AA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * *
1120130 TA GA -A TA TA GTT TT TA GA AA AA TA -A TA TA TA TA GTA TA GTT
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA
* * * * *
1120171 TA -A AA TA TA TA TA -A TA TA GTT TT TCA AA TA TA GT- TT TA -A
1 TA TA TA TA TA TA TA TA TA TA -TA TA T-A TA TA TA -TA TA TA TA
*
1120210 AA TA T- TA GTA 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
1120252 TA TA TA TA TA
1 TA TA TA TA TA
1120262 AAATATGTAG
Statistics
Matches: 201, Mismatches: 29, Indels: 48
0.72 0.10 0.17
Matches are distributed among these distances:
1 12 0.06
2 173 0.86
3 16 0.08
ACGTcount: A:0.49, C:0.01, G:0.07, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1120129 original size:73 final size:74
Alignment explanation
Indices: 1120006--1120167 Score: 206
Period size: 73 Copynumber: 2.2 Consensus size: 74
1119996 TTATAATAAT
* * * *
1120006 TATATATATATAGTA-ATATATAGTATAATATAAATATAATATAAATATATATAGTATATAGTTT
1 TATATATATATAGTATATATATAGTATAATATAAATATAAGAAAAACATATATAGAATATAGTTT
* *
1120070 TTAGGAGAA
66 TTAGAAAAA
* * *
1120079 TATATATATATA-TATATATATA-TATATATATAGATTTTAGAAAAACATATATAGAATATAGTT
1 TATATATATATAGTATATATATAGTATA-ATATAAATATAAGAAAAACATATATAGAATATAGTT
1120142 TTTAGAAAAA
65 TTTAGAAAAA
1120152 TA-ATATATATAGTATA
1 TATATATATATAGTATA
1120168 GTTTAAAATA
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
72 15 0.19
73 62 0.81
ACGTcount: A:0.50, C:0.01, G:0.08, T:0.41
Consensus pattern (74 bp):
TATATATATATAGTATATATATAGTATAATATAAATATAAGAAAAACATATATAGAATATAGTTT
TTAGAAAAA
Found at i:1120143 original size:27 final size:29
Alignment explanation
Indices: 1120096--1120168 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
1120086 ATATATATAT
*
1120096 ATATATATATATATAGATTTTAGAAAAA-C
1 ATATATATA-ATATAGATTTTAGAAAAATA
* *
1120125 ATATATAGAATATAGTTTTTAGAAAAATA
1 ATATATATAATATAGATTTTAGAAAAATA
*
1120154 ATATATATAGTATAG
1 ATATATATAATATAG
1120169 TTTAAAATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
28 17 0.45
29 21 0.55
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.38
Consensus pattern (29 bp):
ATATATATAATATAGATTTTAGAAAAATA
Found at i:1120179 original size:21 final size:21
Alignment explanation
Indices: 1120153--1120192 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1120143 TTAGAAAAAT
*
1120153 AATATATATAGTATAGTTTAA
1 AATATATATAATATAGTTTAA
1120174 AATATATATAATATAGTTT
1 AATATATATAATATAGTTT
1120193 TTCAAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.45
Consensus pattern (21 bp):
AATATATATAATATAGTTTAA
Found at i:1120202 original size:73 final size:71
Alignment explanation
Indices: 1120006--1120261 Score: 181
Period size: 73 Copynumber: 3.4 Consensus size: 71
1119996 TTATAATAAT
* * * * *
1120006 TATATATATATAGTAATATATAGTATAATATAAATATAATATAAATATATATAGTATATAGTTTT
1 TATATATATATA-TAA-ATATA-TAT-ATATAGAT-T-TTAAAAACATATATAGAATATAGTTTT
* *
1120071 TAGGAGAATATA
60 TAGAAAAATATA
*
1120083 TATATATATATATATATATATATATATAGATTTTAGAAAAACATATATAGAATATAGTTTTTAGA
1 TATATATATATATAAATATATATATATAGATTTT--AAAAACATATATAGAATATAGTTTTTAGA
1120148 AAAATAATA
64 AAAAT-ATA
* ** * * * *
1120157 TATATAGTATAGTTTAAAATATATATAATATAG-TTTTTCAAATATAGTTTTAAAATATTAGTAT
1 TATATA-TATA-TAT-AAATATATAT-ATATAGATTTTAAAAACATA--TATAGAATA-TAGTTT
* * * *
1120221 ATATATATATATA
59 TTAGAAAAATATA
*
1120234 TATATATATATATATATATATATATATA
1 TATATATATATATAAATATATATATATA
1120262 AAATATGTAG
Statistics
Matches: 147, Mismatches: 22, Indels: 24
0.76 0.11 0.12
Matches are distributed among these distances:
71 1 0.01
72 1 0.01
73 41 0.28
74 21 0.14
75 17 0.12
76 8 0.05
77 41 0.28
78 17 0.12
ACGTcount: A:0.49, C:0.01, G:0.07, T:0.44
Consensus pattern (71 bp):
TATATATATATATAAATATATATATATAGATTTTAAAAACATATATAGAATATAGTTTTTAGAAA
AATATA
Found at i:1120284 original size:21 final size:21
Alignment explanation
Indices: 1120230--1120291 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
1120220 TATATATATA
* * *
1120230 TATATATATATATATATATA-
1 TATATATATAAAAATATGTAG
1120250 TATATATATATAAAATATGTAG
1 TATATATATA-AAAATATGTAG
*
1120272 TATAGTATTTAAAAATATGT
1 TATA-TATATAAAAATATGT
1120292 TTAAATTGCA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 10 0.29
21 7 0.20
22 13 0.37
23 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (21 bp):
TATATATATAAAAATATGTAG
Found at i:1121351 original size:20 final size:19
Alignment explanation
Indices: 1121322--1121361 Score: 71
Period size: 20 Copynumber: 2.1 Consensus size: 19
1121312 AGTAATCCTA
1121322 TTCCCTGGTAATCTTACAT
1 TTCCCTGGTAATCTTACAT
1121341 TTCCACTGGTAATCTTACAT
1 TTCC-CTGGTAATCTTACAT
1121361 T
1 T
1121362 CCTGCTAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.23, C:0.25, G:0.10, T:0.42
Consensus pattern (19 bp):
TTCCCTGGTAATCTTACAT
Found at i:1121411 original size:87 final size:87
Alignment explanation
Indices: 1121262--1121548 Score: 297
Period size: 87 Copynumber: 3.2 Consensus size: 87
1121252 ACCAAACACA
* *
1121262 GTAATATTATATTCCTGCTAAACCAACCAAACACAAAATACAACATTCCCAGTAATCCTATTCCC
1 GTAATATTACATTCCTGCTAAACCAACCAAACACAAAATACAACATTCCCAGTAATCATATTCCC
*
1121327 TGGTAATCTTACATTTCCACTG
66 TGGTAATCTGACATTTCCACTG
* * *
1121349 GTAATCTTACATTCCTGCTAAACCAACCAAACATAAAATACAACATTCTCAGTAATCATATTCCC
1 GTAATATTACATTCCTGCTAAACCAACCAAACACAAAATACAACATTCCCAGTAATCATATTCCC
1121414 TGGTAATCTGACATTTCAGTAATCTTATTCCCTG
66 TGGTAATCTGACATTTC------C--A----CTG
* * * * *
1121448 GTAATCTTACATTCATGCTAAAACAACCAAACACAAAATACAACATTCTCAGTAATCCTATTCCC
1 GTAATATTACATTCCTGCTAAACCAACCAAACACAAAATACAACATTCCCAGTAATCATATTCCC
* * * *
1121513 CGATGATCTTACA-TTCTCACTG
66 TGGTAATCTGACATTTC-CACTG
* *
1121535 GTGATCTTACATTC
1 GTAATATTACATTC
1121549 TGTGAACCAA
Statistics
Matches: 173, Mismatches: 15, Indels: 24
0.82 0.07 0.11
Matches are distributed among these distances:
87 92 0.53
91 1 0.01
93 3 0.02
95 1 0.01
98 3 0.02
99 73 0.42
ACGTcount: A:0.35, C:0.26, G:0.08, T:0.31
Consensus pattern (87 bp):
GTAATATTACATTCCTGCTAAACCAACCAAACACAAAATACAACATTCCCAGTAATCATATTCCC
TGGTAATCTGACATTTCCACTG
Found at i:1121433 original size:32 final size:33
Alignment explanation
Indices: 1121391--1121461 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 33
1121381 ATAAAATACA
1121391 ACATTCTCAGTAATCATATTCCCTGGTAATCTG
1 ACATTCTCAGTAATCATATTCCCTGGTAATCTG
* *
1121424 ACATT-TCAGTAATCTTATTCCCTGGTAATCTT
1 ACATTCTCAGTAATCATATTCCCTGGTAATCTG
1121456 ACATTC
1 ACATTC
1121462 ATGCTAAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 30 0.86
33 5 0.14
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.39
Consensus pattern (33 bp):
ACATTCTCAGTAATCATATTCCCTGGTAATCTG
Found at i:1121527 original size:99 final size:100
Alignment explanation
Indices: 1121341--1121527 Score: 295
Period size: 99 Copynumber: 1.9 Consensus size: 100
1121331 AATCTTACAT
* * *
1121341 TTCCACTGGTAATCTTACATTCCTGCTAAACCAACCAAACATAAAATACAACATTCTCAGTAATC
1 TTCCACTGGTAATCTTACATTCATGCTAAAACAACCAAACACAAAATACAACATTCTCAGTAATC
* *
1121406 ATATTCCCTGGTAATCTGACATTTCAGTAATCTTA
66 ATATTCCCCGATAATCTGACATTTCAGTAATCTTA
1121441 TTCC-CTGGTAATCTTACATTCATGCTAAAACAACCAAACACAAAATACAACATTCTCAGTAATC
1 TTCCACTGGTAATCTTACATTCATGCTAAAACAACCAAACACAAAATACAACATTCTCAGTAATC
* * *
1121505 CTATTCCCCGATGATCTTACATT
66 ATATTCCCCGATAATCTGACATT
1121528 CTCACTGGTG
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
99 75 0.95
100 4 0.05
ACGTcount: A:0.35, C:0.26, G:0.07, T:0.31
Consensus pattern (100 bp):
TTCCACTGGTAATCTTACATTCATGCTAAAACAACCAAACACAAAATACAACATTCTCAGTAATC
ATATTCCCCGATAATCTGACATTTCAGTAATCTTA
Found at i:1123006 original size:21 final size:19
Alignment explanation
Indices: 1122971--1123017 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
1122961 TATAATTTAT
*
1122971 TATTAT-TTTTTTTATTAC
1 TATTATGTTTATTTATTAC
1122989 TTAATTATGTTTATTTATTAC
1 -T-ATTATGTTTATTTATTAC
1123010 TATTATGT
1 TATTATGT
1123018 ATATATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 8 0.32
20 6 0.24
21 11 0.44
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.66
Consensus pattern (19 bp):
TATTATGTTTATTTATTAC
Found at i:1123688 original size:20 final size:20
Alignment explanation
Indices: 1123665--1123702 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1123655 TATTATTCTA
*
1123665 TTTTTATATTTT-ATTTATG
1 TTTTTTTATTTTGATTTATG
*
1123684 TTTTTTTCTTTTGATTTAT
1 TTTTTTTATTTTGATTTAT
1123703 TTAATGTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.16, C:0.03, G:0.05, T:0.76
Consensus pattern (20 bp):
TTTTTTTATTTTGATTTATG
Found at i:1124322 original size:37 final size:38
Alignment explanation
Indices: 1124281--1124438 Score: 144
Period size: 37 Copynumber: 4.2 Consensus size: 38
1124271 ATTCTAATCG
* *
1124281 AATATTAATTTAT-AATAATATATTCTTATTTTAATTA
1 AATATAAATTCATAAATAATATATTCTTATTTTAATTA
* * **
1124318 AATATAAATTCATAAATAATACATTTTTA-TTTAACCA
1 AATATAAATTCATAAATAATATATTCTTATTTTAATTA
* * * * *
1124355 AATATAAATTTATAAATAATATACTCATATTTCAATTG
1 AATATAAATTCATAAATAATATATTCTTATTTTAATTA
* * * *
1124393 AATATAAATTCAT-AACAACATATT-TAGATTTTAATTG
1 AATATAAATTCATAAATAATATATTCT-TATTTTAATTA
1124430 AATATAAAT
1 AATATAAAT
1124439 CTTCAAATAA
Statistics
Matches: 96, Mismatches: 22, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
37 67 0.70
38 29 0.30
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (38 bp):
AATATAAATTCATAAATAATATATTCTTATTTTAATTA
Found at i:1124434 original size:75 final size:74
Alignment explanation
Indices: 1124275--1124438 Score: 186
Period size: 75 Copynumber: 2.2 Consensus size: 74
1124265 TATTGTATTC
* * * * * *
1124275 TAATCGAATATTAATTTATAATAATATATTCTTATTTTAATTAAATATAAATTCATAAATAATAC
1 TAATCGAATATAAATTTATAATAATATACTCATATTTCAATTAAATATAAATTCATAAACAACAC
**
1124340 ATTTTTATT
66 ATTTAGATT
* * *
1124349 TAACCAAATATAAATTTATAAATAATATACTCATATTTCAATTGAATATAAATTCAT-AACAACA
1 TAATCGAATATAAATTTAT-AATAATATACTCATATTTCAATTAAATATAAATTCATAAACAACA
*
1124413 TATTTAGATTT
65 CATTTAGA-TT
*
1124424 TAATTGAATATAAAT
1 TAATCGAATATAAAT
1124439 CTTCAAATAA
Statistics
Matches: 73, Mismatches: 15, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
74 26 0.36
75 47 0.64
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.43
Consensus pattern (74 bp):
TAATCGAATATAAATTTATAATAATATACTCATATTTCAATTAAATATAAATTCATAAACAACAC
ATTTAGATT
Found at i:1129165 original size:4 final size:4
Alignment explanation
Indices: 1129146--1129179 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
1129136 TAATTATAAA
1129146 TATT ATATT ATATT TATT TATT TATT TATT TATT
1 TATT -TATT -TATT TATT TATT TATT TATT TATT
1129180 AAATTAAGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 20 0.69
5 9 0.31
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:1129653 original size:21 final size:20
Alignment explanation
Indices: 1129629--1129669 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1129619 TAAAAAATTG
* *
1129629 TTTAAAATATTATTATTTTTA
1 TTTAAAACATCATT-TTTTTA
1129650 TTTAAAACATCATTTTTTTA
1 TTTAAAACATCATTTTTTTA
1129670 ATATTTTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTAAAACATCATTTTTTTA
Found at i:1129963 original size:3 final size:3
Alignment explanation
Indices: 1129955--1130006 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
1129945 AAATAGTGAT
1129955 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1130003 ATA A
1 ATA A
1130007 AAAGAGAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1131455 original size:21 final size:21
Alignment explanation
Indices: 1131417--1131463 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
1131407 AGTGCCCAAC
*
1131417 AATAACAAAATCGGTAGAAAA
1 AATAACAAAATCGATAGAAAA
*
1131438 AATAACAAAA-CTGATAGAAAT
1 AATAACAAAATC-GATAGAAAA
1131459 AATAA
1 AATAA
1131464 TATTTCCAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.64, C:0.09, G:0.11, T:0.17
Consensus pattern (21 bp):
AATAACAAAATCGATAGAAAA
Found at i:1132626 original size:10 final size:10
Alignment explanation
Indices: 1132607--1132635 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1132597 TTCTAACATT
1132607 AAAT-AAAAA
1 AAATAAAAAA
1132616 AAATAAAAAA
1 AAATAAAAAA
1132626 AAATAAAAAA
1 AAATAAAAAA
1132636 TGAAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.21
10 15 0.79
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (10 bp):
AAATAAAAAA
Found at i:1133096 original size:21 final size:21
Alignment explanation
Indices: 1133072--1133116 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1133062 TTATTCACTT
1133072 TTTTGGATTTATAAT-ACTGGA
1 TTTTGG-TTTATAATAACTGGA
* *
1133093 TTTTGGTTTGTAATAAGTGGA
1 TTTTGGTTTATAATAACTGGA
1133114 TTT
1 TTT
1133117 ATGCTTGGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.24, C:0.02, G:0.22, T:0.51
Consensus pattern (21 bp):
TTTTGGTTTATAATAACTGGA
Found at i:1136875 original size:18 final size:18
Alignment explanation
Indices: 1136845--1136879 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1136835 CTTTAAAAAC
1136845 ATTATGTTTATTATTATA
1 ATTATGTTTATTATTATA
1136863 ATTAT-TTTGATTATTAT
1 ATTATGTTT-ATTATTAT
1136880 TATAAGTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (18 bp):
ATTATGTTTATTATTATA
Found at i:1136878 original size:21 final size:21
Alignment explanation
Indices: 1136852--1136906 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
1136842 AACATTATGT
1136852 TTATTATTATAATTATT-TTG
1 TTATTATTATAATTATTGTTG
*
1136872 ATTATTATTATAAGTATTGTTG
1 -TTATTATTATAATTATTGTTG
1136894 TTATTATTATAAT
1 TTATTATTATAAT
1136907 AAAATATTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 28 0.90
22 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (21 bp):
TTATTATTATAATTATTGTTG
Found at i:1138370 original size:12 final size:12
Alignment explanation
Indices: 1138355--1138388 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1138345 CTTTTGTTTT
1138355 TTTAATTATTTA
1 TTTAATTATTTA
*
1138367 TTTATTTATTTA
1 TTTAATTATTTA
1138379 -TTAATTATTT
1 TTTAATTATTT
1138389 TTTTGCTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTAATTATTTA
Found at i:1140429 original size:36 final size:36
Alignment explanation
Indices: 1140382--1140451 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
1140372 AAATATGGTG
1140382 ATAGCCCTGTTGTTGTACGTGAAAGTAAACGAACAC
1 ATAGCCCTGTTGTTGTACGTGAAAGTAAACGAACAC
1140418 ATAGCCCTGTTGTTGTACGTGAAAGTAAACGAAC
1 ATAGCCCTGTTGTTGTACGTGAAAGTAAACGAAC
1140452 CCCTGATCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.26
Consensus pattern (36 bp):
ATAGCCCTGTTGTTGTACGTGAAAGTAAACGAACAC
Found at i:1144362 original size:115 final size:116
Alignment explanation
Indices: 1144159--1144389 Score: 439
Period size: 115 Copynumber: 2.0 Consensus size: 116
1144149 GTGGCAGATG
1144159 AAGTAGTTGAAGGGTCTAGCTCCAAGAAAAACCTGTGTACCGGAAAAAGGAAATGAAGTTGCAAG
1 AAGTAGTTGAAGGGTCTAGCTCCAAGAAAAACCTGTGTACCGGAAAAAGGAAATGAAGTTGCAAG
1144224 TATCTACCACAAGAACACTGTAAATAGTGTCACGATAATCCAATCAAGGGC
66 TATCTACCACAAGAACACTGTAAATAGTGTCACGATAATCCAATCAAGGGC
1144275 AAGTAGTTGAAGGGTCTAGCTCC-AG-AAAACCTGTGTACCGGAAAAAGGAAAATGAAGTTGCAA
1 AAGTAGTTGAAGGGTCTAGCTCCAAGAAAAACCTGTGTACCGGAAAAAGG-AAATGAAGTTGCAA
1144338 GTATCTACCACAAGAACACTGTAAATAGTGTCACGATAATCCAATCAAGGGC
65 GTATCTACCACAAGAACACTGTAAATAGTGTCACGATAATCCAATCAAGGGC
1144390 GGAGAGGAAT
Statistics
Matches: 114, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
114 23 0.20
115 68 0.60
116 23 0.20
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (116 bp):
AAGTAGTTGAAGGGTCTAGCTCCAAGAAAAACCTGTGTACCGGAAAAAGGAAATGAAGTTGCAAG
TATCTACCACAAGAACACTGTAAATAGTGTCACGATAATCCAATCAAGGGC
Found at i:1150191 original size:8 final size:8
Alignment explanation
Indices: 1150178--1150236 Score: 59
Period size: 9 Copynumber: 7.2 Consensus size: 8
1150168 TGCTTGAAGA
1150178 AAAAAATG
1 AAAAAATG
*
1150186 AAAAAAATA
1 -AAAAAATG
1150195 AAAAGAATG
1 AAAA-AATG
1150204 AAAAAAT-
1 AAAAAATG
*
1150211 AAAAAAAG
1 AAAAAATG
1150219 AAATAAAT-
1 AAA-AAATG
1150227 AAAAAATG
1 AAAAAATG
1150235 AA
1 AA
1150237 GAGAAAAAGG
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
7 10 0.24
8 15 0.36
9 17 0.40
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:1150226 original size:16 final size:16
Alignment explanation
Indices: 1150177--1150236 Score: 79
Period size: 17 Copynumber: 3.7 Consensus size: 16
1150167 ATGCTTGAAG
1150177 AAAAAAATGAAAAAAAT
1 AAAAAAATG-AAAAAAT
1150194 AAAAAGAATGAAAAAAT
1 AAAAA-AATGAAAAAAT
1150211 AAAAAAA-GAAATAAAT
1 AAAAAAATGAAA-AAAT
1150227 -AAAAAATGAA
1 AAAAAAATGAA
1150237 GAGAAAAAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
15 10 0.25
16 9 0.22
17 17 0.43
18 4 0.10
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (16 bp):
AAAAAAATGAAAAAAT
Found at i:1151303 original size:20 final size:20
Alignment explanation
Indices: 1151240--1151304 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
1151230 TTCAATGGAG
1151240 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
* **
1151260 CA-TCCA-AA-GAGGAAGAAGA
1 -AGTTCATAATGA-GAAGAACT
1151279 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
*
1151299 TGTTCA
1 AGTTCA
1151305 ACCTCGCATC
Statistics
Matches: 33, Mismatches: 7, Indels: 9
0.67 0.14 0.18
Matches are distributed among these distances:
18 3 0.09
19 11 0.33
20 16 0.48
21 3 0.09
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.22
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:1151335 original size:91 final size:91
Alignment explanation
Indices: 1151222--1151400 Score: 297
Period size: 92 Copynumber: 2.0 Consensus size: 91
1151212 AAAGAGATGG
*
1151222 ATCAACATTTCAATGGAGAGTTCATAATGAGAAGAACTCATCC-AAAGAGGAAGAAGAAGTTCAT
1 ATCAACATTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGAAGAAGAAGTTCAA
1151286 AATGAGAAGAACTTGTTCAACCTCGC
66 AATGAGAAGAACTTGTTCAACCTCGC
* * *
1151312 ATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGGGGGAGAAGAAGTTCA
1 ATCAACA-TTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGAAGAAGAAGTTCA
*
1151377 AAATGAGAAGAACTTGTTCGACCT
65 AAATGAGAAGAACTTGTTCAACCT
1151401 ATCACTTGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
90 7 0.09
91 36 0.44
92 39 0.48
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (91 bp):
ATCAACATTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGAAGAAGAAGTTCAA
AATGAGAAGAACTTGTTCAACCTCGC
Found at i:1151675 original size:135 final size:135
Alignment explanation
Indices: 1151316--1151659 Score: 511
Period size: 135 Copynumber: 2.6 Consensus size: 135
1151306 CCTCGCATCA
* * * * * *
1151316 ACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGGGGGAGAAGAAGTTCAAAAT
1 ACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCAACA-AGGAAGAAGAAGTTCATAAT
*
1151381 GAGAAGAACTTGTTCGACCTATCACTTGATTCATGACATTTCGAATCAGTGACACCTCGCTTGAG
65 GAGAAGAACTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCGCTTGAG
1151446 GGATTG
130 GGATTG
1151452 ACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCAACAAGGAAGAAGAAGTTCATAATG
1 ACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCAACAAGGAAGAAGAAGTTCATAATG
* * * * *
1151517 AGAAGAGCTTGTTCGACCTATCACTCGATTCATGGCATTTCGAATTAGTGACGCCTCGTTTGAGG
66 AGAAGAACTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCGCTTGAGG
1151582 GATTG
131 GATTG
* *
1151587 ACATTTCC-A-GAAGAGTTCATAATGAGAAGAACTCGTCCTA-AAGG-AG-A-AAGTTCATAATG
1 ACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCAACAAGGAAGAAGAAGTTCATAATG
1151646 AGAAGAACTTGTTC
66 AGAAGAACTTGTTC
1151660 CTTTCAAGTC
Statistics
Matches: 193, Mismatches: 15, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
129 25 0.13
130 1 0.01
131 2 0.01
132 4 0.02
133 29 0.15
134 1 0.01
135 90 0.47
136 41 0.21
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (135 bp):
ACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCAACAAGGAAGAAGAAGTTCATAATG
AGAAGAACTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCGCTTGAGG
GATTG
Found at i:1151859 original size:90 final size:89
Alignment explanation
Indices: 1151695--1151862 Score: 239
Period size: 90 Copynumber: 1.9 Consensus size: 89
1151685 TGGATCAACA
* * * * * *
1151695 TTTCCAGTGGAGTGTTCATAATGAGAAGAACTCGTCCAATGGGGGAGAAGAAGTTCATAATGAGA
1 TTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCCAA--GGAGAGAAGAAATTCATAATAAGA
1151760 AGAACTTGTTCAACCTTGCATCAGTG
64 AGAACTTGTTCAACCTTGCATCAGTG
1151786 TTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCTACAA-GAGAGAAGAAATTCATAATAAGA
1 TTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATC--CAAGGAGAGAAGAAATTCATAATAAGA
1151850 AGAACTTGTTCAA
64 AGAACTTGTTCAA
1151863 TCAAATAACG
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
90 33 0.48
91 33 0.48
93 3 0.04
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.26
Consensus pattern (89 bp):
TTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCCAAGGAGAGAAGAAATTCATAATAAGAAG
AACTTGTTCAACCTTGCATCAGTG
Found at i:1152004 original size:3 final size:3
Alignment explanation
Indices: 1151996--1152052 Score: 53
Period size: 3 Copynumber: 19.0 Consensus size: 3
1151986 AACATTATGT
* * * * *
1151996 TTA TTA TTA TAA TTA TT- TTGA TTA TTA TTA TTA TAA GTA TTT TTG
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
1152041 TTA TTA TTA TTA
1 TTA TTA TTA TTA
1152053 ATAATAATAT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
2 2 0.05
3 39 0.91
4 2 0.05
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1152028 original size:24 final size:24
Alignment explanation
Indices: 1151996--1152057 Score: 90
Period size: 24 Copynumber: 2.5 Consensus size: 24
1151986 AACATTATGT
1151996 TTATTATTATAATTA-TTTTGATTA
1 TTATTATTATAATTATTTTTG-TTA
*
1152020 TTATTATTATAAGTATTTTTGTTA
1 TTATTATTATAATTATTTTTGTTA
1152044 TTATTATTAATAAT
1 TTATTATT-ATAAT
1152058 AATATTACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
24 25 0.74
25 9 0.26
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (24 bp):
TTATTATTATAATTATTTTTGTTA
Found at i:1159967 original size:2 final size:2
Alignment explanation
Indices: 1159960--1159994 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1159950 CTTCAAATAC
* *
1159960 AT AT AT AT AT AT AT AT AT AT AC AT AT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1159995 ATAATGTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1160651 original size:21 final size:21
Alignment explanation
Indices: 1160551--1160651 Score: 96
Period size: 21 Copynumber: 4.7 Consensus size: 21
1160541 AAAGTGCCAT
*
1160551 AGTACACAAAGTAGTACTACA
1 AGTACACAAAGTACTACTACA
* *
1160572 AGTGCACAAAGTAGTACTACA
1 AGTACACAAAGTACTACTACA
* *
1160593 AGTACACAAAATACT-CTTGTCA
1 AGTACACAAAGTACTAC-T-ACA
* *
1160615 TAGTACACGAAGTACTACTCCA
1 -AGTACACAAAGTACTACTACA
*
1160637 AGTACACAAATTACT
1 AGTACACAAAGTACT
1160652 CTTACGAAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
20 1 0.02
21 46 0.70
22 4 0.06
23 14 0.21
24 1 0.02
ACGTcount: A:0.43, C:0.22, G:0.13, T:0.23
Consensus pattern (21 bp):
AGTACACAAAGTACTACTACA
Found at i:1169196 original size:15 final size:15
Alignment explanation
Indices: 1169178--1169212 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
1169168 AAATCATTGG
1169178 AAGTCGACTCATCAC
1 AAGTCGACTCATCAC
1169193 AAGTCGACTCATCAC
1 AAGTCGACTCATCAC
1169208 AAGTC
1 AAGTC
1169213 TTCTTCCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.34, C:0.31, G:0.14, T:0.20
Consensus pattern (15 bp):
AAGTCGACTCATCAC
Found at i:1172877 original size:42 final size:42
Alignment explanation
Indices: 1172813--1172931 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
1172803 TTCCCCGAAA
**
1172813 TCCCGTGTTTGTTTCATATAATTCGTTTTCCGGAAAATGTTT
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTT
* **
1172855 TCCCGTGTTTGTTTCACGTAATTCGTTTTTCAAAAAATGTTT
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTT
1172897 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1172932 CGTAATTCAT
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.18, C:0.18, G:0.17, T:0.46
Consensus pattern (42 bp):
TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTT
Found at i:1173149 original size:22 final size:23
Alignment explanation
Indices: 1173102--1173162 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
1173092 TAATTATTAA
* *
1173102 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
1173123 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
1173146 -ATATTTTTAATATTATA
1 AATATTTATAATAATATA
1173163 TAAAATAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.32
22 19 0.56
23 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:1173225 original size:54 final size:52
Alignment explanation
Indices: 1173128--1173230 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 52
1173118 TTATTAATAT
*
1173128 TTATAATAATATAATATTATATTTTTAATATTATATAAAATAATCAATTATA
1 TTATAATAATATAATATTATATTTTTAATATTATATAAAATAATAAATTATA
*
1173180 TTATAATAATATAAGATATTATATTTTT-ATTTTA-ATAATATATAATAAATT
1 TTATAATAATAT-A-ATATTATATTTTTAATATTATATAA-A-ATAATAAATT
1173231 TTTTATATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
52 16 0.36
53 7 0.16
54 22 0.49
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (52 bp):
TTATAATAATATAATATTATATTTTTAATATTATATAAAATAATAAATTATA
Found at i:1173283 original size:24 final size:28
Alignment explanation
Indices: 1173215--1173277 Score: 85
Period size: 27 Copynumber: 2.2 Consensus size: 28
1173205 TTTATTTTAA
*
1173215 TAATATAT-AATAAATTT-TTTATATATT
1 TAATA-ATGAATAATTTTATTTATATATT
1173242 TAATAATGAATAATTTTATTTATATATT
1 TAATAATGAATAATTTTATTTATATATT
1173270 TAAATAAT
1 T-AATAAT
1173278 ATTTTAGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 2 0.06
27 13 0.41
28 11 0.34
29 6 0.19
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (28 bp):
TAATAATGAATAATTTTATTTATATATT
Found at i:1173407 original size:90 final size:86
Alignment explanation
Indices: 1173295--1173464 Score: 202
Period size: 90 Copynumber: 1.9 Consensus size: 86
1173285 TAAAGATATT
* * * *
1173295 TAAAATATACTAATTAATATTTTTA-AAATATAA-TATAACAAA-ATTACTTTAATAAATAATTA
1 TAAAATATACAAATTAATATTTTTATAAATAAAATTATAA-AAATAATA-TTTAAT-AATAAATA
1173357 ATATAATTTATAATATTTTATTTCAC
63 A-ATAATTT-TAATATTTTATTTCAC
*
1173383 TAAAATATACCAATATTAATATTTTTATTAATAAAATTATAAAAATAATATTTAATAATAAATAA
1 TAAAATATA-CAA-ATTAATATTTTTATAAATAAAATTATAAAAATAATATTTAATAATAAATAA
*
1173448 ATTATTTTAATATTTTA
64 ATAATTTTAATATTTTA
1173465 AAATAATAAT
Statistics
Matches: 71, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
88 19 0.27
89 8 0.11
90 21 0.30
91 15 0.21
92 8 0.11
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (86 bp):
TAAAATATACAAATTAATATTTTTATAAATAAAATTATAAAAATAATATTTAATAATAAATAAAT
AATTTTAATATTTTATTTCAC
Found at i:1173633 original size:20 final size:20
Alignment explanation
Indices: 1173608--1173651 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
1173598 TTTCCAGATG
1173608 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
1173628 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
1173648 TTTT
1 TTTT
1173652 TCAAAATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:1173673 original size:29 final size:30
Alignment explanation
Indices: 1173640--1173717 Score: 113
Period size: 30 Copynumber: 2.6 Consensus size: 30
1173630 TTCCAGAAAT
* *
1173640 GTAATTCATTTTTCA-AAATTCAAATTCCA
1 GTAATTCATTTTCCAGAAATTCAAATTACA
*
1173669 GTAATTCATTTTCCAGTAATTCAAATTACA
1 GTAATTCATTTTCCAGAAATTCAAATTACA
*
1173699 GTAATTCATTTTCCGGAAA
1 GTAATTCATTTTCCAGAAA
1173718 ACCAATTACA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 14 0.33
30 29 0.67
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.40
Consensus pattern (30 bp):
GTAATTCATTTTCCAGAAATTCAAATTACA
Found at i:1173676 original size:15 final size:15
Alignment explanation
Indices: 1173656--1173706 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
1173646 CATTTTTCAA
1173656 AATTCAAATTCCAGT
1 AATTCAAATTCCAGT
**
1173671 AATTCATTTTCCAGT
1 AATTCAAATTCCAGT
*
1173686 AATTCAAATTACAGT
1 AATTCAAATTCCAGT
1173701 AATTCA
1 AATTCA
1173707 TTTTCCGGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.37
Consensus pattern (15 bp):
AATTCAAATTCCAGT
Found at i:1175276 original size:2 final size:2
Alignment explanation
Indices: 1175269--1175298 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1175259 AATAACATTC
1175269 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
1175299 CCATAAGTGA
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):
AT
Found at i:1178890 original size:826 final size:828
Alignment explanation
Indices: 1177297--1178955 Score: 2993
Period size: 826 Copynumber: 2.0 Consensus size: 828
1177287 CATGAAGACA
* *
1177297 ATAGCTTTAACCAAAGGTAGGGGGCTATAGTATGCATGTGAATCGAGAACTAATTTAAAAGCTTT
1 ATAGCTTTAACCAAAGATAGGGGGCTATAGTATGCATGAGAATCGAGAACTAATTTAAAAGCTTT
1177362 AGCACTATTATATTGCATTTTAGCTTTAATGTTTTATTTTAAAATAAAAATATTTTTTAAATGAA
66 AGCACTATTATATTGCATTTTAGCTTTAATGTTTTATTTTAAAATAAAAATATTTTTTAAATGAA
* * *
1177427 AATTATTAATAAAAAATATTAATGTTCTAAAATAAAGGTCATTTTACCCGGATGATATATTGGAA
131 AATTATTAATAAAAAATATTAATGTTATAAAATAAAGGTCACTTTACCCGGAAGATATATTGGAA
1177492 GCTAAAATGTTCCCTTAGAAAATAATAAGATCAAACTACTATTTAATCAAACATGTAACACCTAC
196 GCTAAAATGTTCCCTTAGAAAATAATAAGATCAAACTACTATTTAATCAAACATGTAACACCTAC
*
1177557 GACCCATATATTTTTACCAATACAGGTTATAGATATCACATGATTTACTTAAAACATTTCCCAAT
261 GACCCATATATTTATACCAATACAGGTTATAGATATCACATGATTTACTTAAAACATTTCCCAAT
1177622 TCAAAAGCGGCTTGAAAATTTTTTCTTTTCAATTATAATAGAAAATATAAAATAATAAATCACAT
326 TCAAAAGCGGCTTGAAAATTTTTTCTTTTCAATTATAATAGAAAATATAAAATAATAAATCACAT
1177687 AATTTTTTTATATAATATTTAAATATCAAATACGTTCATTTATAAAAGTAATACTAAATAATATC
391 AATTTTTTTATATAATATTTAAATATCAAATACGTTCATTTATAAAAGTAATACTAAATAATATC
* *
1177752 ATCCATGATGAAATAGAGTAAAACAATTTAGTTTAGTCATTACAACTATTTCCAAAATAATTAAC
456 ATCCATGATGAAATAGAGTAAAACAATTTAGTTTAGCCATTAAAACTATTTCCAAAATAATTAAC
*
1177817 AAAGCAACTAGAACATTTATAAGTACATGCCACTAAATAAGTCAGAATTACATCAAAGGACGTCT
521 AAAGCAACTAGAACATTTATAAGTACATGCCACTAAATAAGTCAGAATTACATCAAAGAACGTCT
* * *
1177882 TATTGATATTGTATTATACTACTCGATGCTTGATGTTGCTCAGTACTCCTTACTTCTACTCCTGA
586 TACTAATATTGTATTATAATACTCGATGCTTGATGTTGCTCAGTACTCCTTACTTCTACTCCTGA
* *
1177947 CGTTTATATACGCGTGAAAATCATCACACGTTAAGTATATACTTAGTGAAACAATTTAAAAATAA
651 CGTTTACATACGCGTGAAAATCATCACACGCTAAGTATATACTTAGTGAAACAATTTAAAAATAA
1178012 TAAACAATCATTTCATGCATAAAATTTAAATGTCATCATCAAATACCATAAGATTTTATTACCTG
716 TAAACAATCATTTCATGCATAAAATTTAAATGTCATCATCAAATACCATAAGATTTTATTACCTG
*
1178077 CG-AAAATCAACATGACATGTTATAAATATAGTAATTTAATCAATAACT
781 -GAAAAATCAACATGACATGTTATAAATATAATAATTTAATCAATAACT
* *
1178125 ATAGCTTTAACCAAAGATAGGGGGCTATTGTATGCATGAGAATCGAGAACTAATTTAATAGCTTT
1 ATAGCTTTAACCAAAGATAGGGGGCTATAGTATGCATGAGAATCGAGAACTAATTTAAAAGCTTT
*
1178190 AGCACTATTATATTGCATTTTAGCTTTAATGTTTTATTTTAAAATAAAAATCTTTTTTAAATGAA
66 AGCACTATTATATTGCATTTTAGCTTTAATGTTTTATTTTAAAATAAAAATATTTTTTAAATGAA
1178255 AATTATTAATAAACAAATATTAATGTTATAAAATAAAGGTCACTTTACCCGGAAGATATATTGGA
131 AATTATTAATAAA-AAATATTAATGTTATAAAATAAAGGTCACTTTACCCGGAAGATATATTGGA
1178320 AGCTAAAATGTTCCCTTAGAAAATAATAAGATCAAACTACTATTTAATC-AA-A-GTAACACCTA
195 AGCTAAAATGTTCCCTTAGAAAATAATAAGATCAAACTACTATTTAATCAAACATGTAACACCTA
*
1178382 CGACCCATATATTTATACCAATACAGGTTATAGATATCACATGATTTACTTAAAACATTTCTCAA
260 CGACCCATATATTTATACCAATACAGGTTATAGATATCACATGATTTACTTAAAACATTTCCCAA
* **
1178447 TTCAAAAGTGGCTTGAATTTTTTTTCTTTTCAATTATAATAGAAAATATAAAATAATAAATCACA
325 TTCAAAAGCGGCTTGAAAATTTTTTCTTTTCAATTATAATAGAAAATATAAAATAATAAATCACA
*
1178512 TTATTTTTTTATATAATATTTAAATATCAAATACGTTCATTTATAAAAGTAATACTAAATAATAT
390 TAATTTTTTTATATAATATTTAAATATCAAATACGTTCATTTATAAAAGTAATACTAAATAATAT
*
1178577 CATCCATGATGAAATAGAGTAAAACAATTTAGTTTAGCCATTAAAACTATTTCCAAAATAGTTAA
455 CATCCATGATGAAATAGAGTAAAACAATTTAGTTTAGCCATTAAAACTATTTCCAAAATAATTAA
1178642 CAAAGCAACTAGAACATTTATAAGTACATGCCACTAAATAAGTCAGAATTACATCAAAGAACGTC
520 CAAAGCAACTAGAACATTTATAAGTACATGCCACTAAATAAGTCAGAATTACATCAAAGAACGTC
* *
1178707 TTACTAATATTGTATTATAATCCTCGATGCTTGGTGTTGCTCAGTACTCCTTACTTCTACTCCTG
585 TTACTAATATTGTATTATAATACTCGATGCTTGATGTTGCTCAGTACTCCTTACTTCTACTCCTG
* **
1178772 ACGTTTACATACGCGTGAAAATTATCACACGCTAAGTATATACTTAGTGATGCAATTTAAAAATA
650 ACGTTTACATACGCGTGAAAATCATCACACGCTAAGTATATACTTAGTGAAACAATTTAAAAATA
* *
1178837 ATAAATAATCATTTCATGCATAAAATTTAAATGTCATCATCAAATACCATAAGATTTTCTTACCT
715 ATAAACAATCATTTCATGCATAAAATTTAAATGTCATCATCAAATACCATAAGATTTTATTACCT
1178902 GGAAAAATCAACATGACATGTTATAAATATAATAATTTAATCAATAACT
780 GGAAAAATCAACATGACATGTTATAAATATAATAATTTAATCAATAACT
1178951 ATAGC
1 ATAGC
1178956 CCAATTTATT
Statistics
Matches: 798, Mismatches: 31, Indels: 6
0.96 0.04 0.01
Matches are distributed among these distances:
825 1 0.00
826 559 0.70
827 1 0.00
828 140 0.18
829 97 0.12
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (828 bp):
ATAGCTTTAACCAAAGATAGGGGGCTATAGTATGCATGAGAATCGAGAACTAATTTAAAAGCTTT
AGCACTATTATATTGCATTTTAGCTTTAATGTTTTATTTTAAAATAAAAATATTTTTTAAATGAA
AATTATTAATAAAAAATATTAATGTTATAAAATAAAGGTCACTTTACCCGGAAGATATATTGGAA
GCTAAAATGTTCCCTTAGAAAATAATAAGATCAAACTACTATTTAATCAAACATGTAACACCTAC
GACCCATATATTTATACCAATACAGGTTATAGATATCACATGATTTACTTAAAACATTTCCCAAT
TCAAAAGCGGCTTGAAAATTTTTTCTTTTCAATTATAATAGAAAATATAAAATAATAAATCACAT
AATTTTTTTATATAATATTTAAATATCAAATACGTTCATTTATAAAAGTAATACTAAATAATATC
ATCCATGATGAAATAGAGTAAAACAATTTAGTTTAGCCATTAAAACTATTTCCAAAATAATTAAC
AAAGCAACTAGAACATTTATAAGTACATGCCACTAAATAAGTCAGAATTACATCAAAGAACGTCT
TACTAATATTGTATTATAATACTCGATGCTTGATGTTGCTCAGTACTCCTTACTTCTACTCCTGA
CGTTTACATACGCGTGAAAATCATCACACGCTAAGTATATACTTAGTGAAACAATTTAAAAATAA
TAAACAATCATTTCATGCATAAAATTTAAATGTCATCATCAAATACCATAAGATTTTATTACCTG
GAAAAATCAACATGACATGTTATAAATATAATAATTTAATCAATAACT
Found at i:1181106 original size:29 final size:30
Alignment explanation
Indices: 1181058--1181121 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
1181048 ATTTCGGTCC
** *
1181058 CTAAACTTTTCAAAGTTTATGCTTCAGCCA
1 CTAAACTTTTCAAAACTTATACTTCAGCCA
* *
1181088 CTAAAC-TTTCAAAACTTATACTTTAGTCA
1 CTAAACTTTTCAAAACTTATACTTCAGCCA
1181117 CTAAA
1 CTAAA
1181122 TAAAATTTGG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 23 0.79
30 6 0.21
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (30 bp):
CTAAACTTTTCAAAACTTATACTTCAGCCA
Found at i:1193185 original size:35 final size:35
Alignment explanation
Indices: 1193129--1193202 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
1193119 CACATTCCTC
*
1193129 AATTTCATTCTAAACCCTAAATT-TCAAAATAATTT
1 AATTACATTCTAAACCCTAAATTCT-AAAATAATTT
* *
1193164 AATTACATTTTAAACCCTAAATTCTAAAATACTTT
1 AATTACATTCTAAACCCTAAATTCTAAAATAATTT
1193199 AATT
1 AATT
1193203 TAAGGTTTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
35 34 0.97
36 1 0.03
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (35 bp):
AATTACATTCTAAACCCTAAATTCTAAAATAATTT
Found at i:1193245 original size:35 final size:35
Alignment explanation
Indices: 1193206--1193273 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
1193196 TTTAATTTAA
* *
1193206 GGTTTAGAATGTAATTGAAGTATTCTAGAATTTGG
1 GGTTTAAAATGTAATTGAAATATTCTAGAATTTGG
* * *
1193241 GGTTTAAAATGTAGTTGAAATGTTTTAGAATTT
1 GGTTTAAAATGTAATTGAAATATTCTAGAATTT
1193274 TGAACATGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.32, C:0.01, G:0.24, T:0.43
Consensus pattern (35 bp):
GGTTTAAAATGTAATTGAAATATTCTAGAATTTGG
Found at i:1194177 original size:21 final size:21
Alignment explanation
Indices: 1194151--1194192 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1194141 TACTATAGGG
1194151 GTATCGATAC-CTTGCTACAGT
1 GTATCGATACTC-TGCTACAGT
1194172 GTATCGATACTCTGCTACAGT
1 GTATCGATACTCTGCTACAGT
1194193 AATTTCGGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (21 bp):
GTATCGATACTCTGCTACAGT
Found at i:1194771 original size:22 final size:22
Alignment explanation
Indices: 1194754--1194806 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
1194744 AAATTTCTCT
1194754 CGAATGACCTATGTATTTGTCC
1 CGAATGACCTATGTATTTGTCC
* *
1194776 CGAATGGCCTTTGTATTTGTCC
1 CGAATGACCTATGTATTTGTCC
1194798 CGAATGACC
1 CGAATGACC
1194807 GCGTAGACCC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.34
Consensus pattern (22 bp):
CGAATGACCTATGTATTTGTCC
Found at i:1195006 original size:21 final size:21
Alignment explanation
Indices: 1194960--1195006 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
1194950 CACATGTATG
** *
1194960 TGTA-AACATATATGTCATTT
1 TGTATAACATATATCACATAT
*
1194980 TATATAACATATATCACATAT
1 TGTATAACATATATCACATAT
1195001 TGTATA
1 TGTATA
1195007 TTCATGTAGA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (21 bp):
TGTATAACATATATCACATAT
Found at i:1195067 original size:44 final size:44
Alignment explanation
Indices: 1195019--1195102 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 44
1195009 CATGTAGATC
* * *
1195019 ATATCATATTCTCATATGGTCACATAGATCATATCACATAGCTG
1 ATATCATATTCTCATATCGTCACATAAATCATATAACATAGCTG
* * * *
1195063 ATATCTTGTTCTCATATCTTCACATAAATCTTATAACATA
1 ATATCATATTCTCATATCGTCACATAAATCATATAACATA
1195103 TAACTCCTCA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
44 33 1.00
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (44 bp):
ATATCATATTCTCATATCGTCACATAAATCATATAACATAGCTG
Found at i:1200323 original size:12 final size:12
Alignment explanation
Indices: 1200306--1200330 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1200296 ATAAGAATAT
1200306 TGTAACTACAAA
1 TGTAACTACAAA
1200318 TGTAACTACAAA
1 TGTAACTACAAA
1200330 T
1 T
1200331 ATAGGACCTC
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:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (12 bp):
TGTAACTACAAA
Found at i:1201336 original size:36 final size:36
Alignment explanation
Indices: 1201265--1201337 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 36
1201255 GTTAAAAAAT
*
1201265 ATTTATATATTTTCTTTAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAATCATAAA
*
1201301 ATTTATATAATTTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATT-AAAATCATAAA
1201337 A
1 A
1201338 AGATTTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 24 0.73
37 9 0.27
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAAATTAAAATCATAAA
Found at i:1204846 original size:201 final size:200
Alignment explanation
Indices: 1204081--1205053 Score: 1115
Period size: 201 Copynumber: 4.8 Consensus size: 200
1204071 TAAAATTTTC
* * *
1204081 CATAAAGTGTCGATAAATTTTTAAAAAGTATCGATCCAAAAAATATCGAAACCGAAAATTATAAT
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATAAT
* * **
1204146 GTAATAGGTAAATTTACAATGTGACCGGTATAAATATACCGATTTTATGAGAAAATAGGTCAGTA
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGT-AACA
* ** * * ** *
1204211 TAAAGTATCGACACCAT-TTAAATTTGTGTCGATATTTTTTGTGCGAGGCT-TTGTTTACTCAAC
130 TAATGTATCGACA-CATGTTAAATTTGTGTCGATACATTTTGTGCCA---TAATGAATGCTCAAC
* *
1204274 AAGGTGCACA
191 GAGGTGCACG
* * * *
1204284 CATAAAGTATCGATATAATTATTAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATAAT
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATAAT
* * **
1204349 GTAATAGTTAAATTTACAATGTAACCGATATAAATATACATGTTTTATGAGAAAATAGGTATACA
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTA-ACA
* * * *
1204414 TAATGTATTGGCAC-TGTTTAAATTTGTGTCGATACATTTTGT-CCATAATGAATGGC-AAACGG
130 TAATGTATCGACACATG-TTAAATTTGTGTCGATACATTTTGTGCCATAATGAAT-GCTCAACGA
*
1204476 GGTGCACT
193 GGTGCACG
* ** * * *
1204484 CATAAAGTGTCGATACATTT-GAAATTGTATTGATCCCAAAAACATCGAAACCGATAATTATAAT
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATAAT
* * * ** *
1204548 GTAATACGTAAATTTATAATGTAACTGGTATAAATATATTGGTTTTATGAGAAAATATGTATACA
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTA-ACA
*
1204613 TAATGTATCGACA-ATGTTTAAATTTGTGTCGATACATTTTGT-CCATAATGAATGC-CAAACGG
130 TAATGTATCGACACATG-TTAAATTTGTGTCGATACATTTTGTGCCATAATGAATGCTC-AACGA
1204675 GGTGCACG
193 GGTGCACG
* * * *
1204683 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAAATATTGAAACCTATAATTATAA
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGAT-CCAAAAAACATCGAAACCGAAAATTATAA
* * * * * *
1204748 TGTAATAGGTAATTTTGCAATGTAACCGATATAAATATACCGGTTTAATTAGAAAATCGGTCAAC
65 TGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGT-AAC
* ** * * * **
1204813 ATAATGTATCGACACTTGTTAAATTTGTGTCGATATTTTTTGTGCGAGACTTTGTTTGCTCAACG
129 ATAATGTATCGACACATGTTAAATTTGTGTCGATACATTTTGTGCCATA--ATGAATGCTCAACG
1204878 AGGTGCACG
192 AGGTGCACG
* *
1204887 CATAAAGTGTCGAT--ATTTATTAAAAGTATTGATCCAAAAAACATCGAAACCGAAAATTATAAT
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATAAT
* *
1204950 GTAATAGGTAAATTTACAATATAATCGGTATAAATATACCGGTTTTATGAGAAAATAGGTTAACA
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGG-TAACA
* *
1205015 TAATGTATCGACAC-TTTTAAATTTGTGTCGATACGTTTT
130 TAATGTATCGACACATGTTAAATTTGTGTCGATACATTTT
1205054 TAAATTACAC
Statistics
Matches: 657, Mismatches: 97, Indels: 35
0.83 0.12 0.04
Matches are distributed among these distances:
198 2 0.00
199 176 0.27
200 62 0.09
201 210 0.32
202 28 0.04
203 147 0.22
204 31 0.05
205 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (200 bp):
CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATAAT
GTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTAACAT
AATGTATCGACACATGTTAAATTTGTGTCGATACATTTTGTGCCATAATGAATGCTCAACGAGGT
GCACG
Found at i:1209414 original size:177 final size:177
Alignment explanation
Indices: 1209104--1209448 Score: 473
Period size: 177 Copynumber: 1.9 Consensus size: 177
1209094 AGCTAAATAT
1209104 GTGTCGATACACTTTCTAAAAGTATCGACCCTAAAAACATCGAAACCAATAATTATAATGTAATA
1 GTGTCGATACACTTTCTAAAAGTATCGACCCTAAAAACATCGAAACCAATAATTATAATGTAATA
* * *
1209169 GGTAAATTAACAATGTAACCGGTATAAATATACCGGTTAATTAGAAAACAGATCAACATAATGTA
66 GGTAAATTAACAATGTAACCAGTATAAATATACCGGTTAATGAGAAAACAGATCAACATAAAGTA
* *
1209234 TCGACA-CTTTTGGAATTTGTGTCGATACTTATTGTCCAGAATATAAA
131 TCGACACCATTT-AAATTTGTGTCGATACTTATTGTCCAGAATATAAA
* * *
1209281 GTGTCGATACA-TTTATTAAAAGTATCGATCCC-AATAACATCGAAACCGATAATTATAATGTAA
1 GTGTCGATACACTTT-CTAAAAGTATCGA-CCCTAAAAACATCGAAACCAATAATTATAATGTAA
* * * * * * * *
1209344 TAGGTGAATTTACAATGTAACTAGTATAAATATACTGGTTTTATGAGAAAATAGGT-AGCATAAA
64 TAGGTAAATTAACAATGTAACCAGTATAAATATACCGG-TTAATGAGAAAACAGATCAACATAAA
*
1209408 GTATCGACACCATTTAAATTTGTGTCGATACTTTTTGTCCA
128 GTATCGACACCATTTAAATTTGTGTCGATACTTATTGTCCA
1209449 TAATGAATGC
Statistics
Matches: 147, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
176 3 0.02
177 124 0.84
178 20 0.14
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (177 bp):
GTGTCGATACACTTTCTAAAAGTATCGACCCTAAAAACATCGAAACCAATAATTATAATGTAATA
GGTAAATTAACAATGTAACCAGTATAAATATACCGGTTAATGAGAAAACAGATCAACATAAAGTA
TCGACACCATTTAAATTTGTGTCGATACTTATTGTCCAGAATATAAA
Found at i:1209655 original size:199 final size:198
Alignment explanation
Indices: 1209276--1209782 Score: 630
Period size: 199 Copynumber: 2.5 Consensus size: 198
1209266 TGTCCAGAAT
* *
1209276 ATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCAATAACATCGAAACCGATAATTATAATG
1 ATAAAGTGTCGATACATTTATTAAAAGTATCGAT-CCAAAAACATCAAAACCGATAATTATAATG
* * * * * *
1209341 TAATAGGTGAATTTACAATGTAACTAGTATAAATATACTGGTTTTATGAGAAAATAGGTAGCATA
65 TAATAGGTAAATTTACAATGTACCGAGTATAAATATACCGGTTTTATGAGAAAATAGCTAGAATA
* *
1209406 AAGTATCGACACCATTTAAATTTGTGTCGATACTTTTTGTCCATAATGAATGCCAAACGGGGTGC
130 AAGTATCGACACCATTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGAGGTGC
1209471 ACAC
195 ACAC
*
1209475 ATAAAGTGTCGATACATTTATTAAAAGTATCGATCGCAAAAACATCAAAACCGATAATTACAATG
1 ATAAAGTGTCGATACATTTATTAAAAGTATCGATC-CAAAAACATCAAAACCGATAATTATAATG
* * *
1209540 TGATAGGTAAATTTACAATGTACCGAATAGAAATATACCGGTTTTATGAGAAAATATGCCTA-AA
65 TAATAGGTAAATTTACAATGTACCGAGTATAAATATACCGGTTTTATGAGAAAATA-G-CTAGAA
* * ** * * *
1209604 TTATGTATCGACACTTTTTAACTTTGTGTCGATACTTTTT-TCCAGAATGAATGCCCAATGAGGT
128 TAAAGTATCGACACCATTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGAGGT
**
1209668 GCATGC
193 GCACAC
* *
1209674 ATAAAGTGTCGATACATTTA--AAATTGTATCGATCCAAAAAAACATCGAAAA-TGATAATTATA
1 ATAAAGTGTCGATACATTTATTAAA-AGTATCGATCC--AAAAACATC-AAAACCGATAATTATA
* * * *
1209736 ATATAATAGATAAATTTGCAATGTTACCG-GTATAAATATACCAGTTT
62 ATGTAATAGGTAAATTTACAATG-TACCGAGTATAAATATACCGGTTT
1209783 ACTTAGATAA
Statistics
Matches: 267, Mismatches: 33, Indels: 16
0.84 0.10 0.05
Matches are distributed among these distances:
197 4 0.01
198 10 0.04
199 205 0.77
200 46 0.17
201 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (198 bp):
ATAAAGTGTCGATACATTTATTAAAAGTATCGATCCAAAAACATCAAAACCGATAATTATAATGT
AATAGGTAAATTTACAATGTACCGAGTATAAATATACCGGTTTTATGAGAAAATAGCTAGAATAA
AGTATCGACACCATTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGAGGTGCA
CAC
Found at i:1209880 original size:64 final size:64
Alignment explanation
Indices: 1209812--1209939 Score: 193
Period size: 64 Copynumber: 2.0 Consensus size: 64
1209802 ATAAGCGCTA
* *
1209812 CCTATTACATTATATAAGGGCTACCTAATATGTTATTGTATTTAATAATATTTCCGGTTAAATG
1 CCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTAATAATATTTCCGGTTAAATG
** * * *
1209876 CCTATTTTATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTTTCGGTTAAATG
1 CCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTAATAATATTTCCGGTTAAATG
1209940 ATATAACATA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (64 bp):
CCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTAATAATATTTCCGGTTAAATG
Found at i:1210236 original size:20 final size:20
Alignment explanation
Indices: 1210211--1210448 Score: 237
Period size: 20 Copynumber: 11.6 Consensus size: 20
1210201 TAGTTGAAAA
1210211 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * *
1210231 TCGCGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCATT
1210253 T-GTCGTTGCGATTTTCCATT
1 TCG-CGTTGCGATTTTCCATT
* ** **
1210273 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
* ** **
1210294 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
*
1210315 TCGCGTTGCGATTTTCTATT
1 TCGCGTTGCGATTTTCCATT
1210335 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
1210355 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
1210375 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * *
1210395 TCGCGTTGCGATAGTCTACA-G
1 TCGCGTTGCGAT--TTTCCATT
1210416 TCGTCGTTGCGATTTTCCATT
1 TCG-CGTTGCGATTTTCCATT
1210437 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1210449 AATCTACAGT
Statistics
Matches: 186, Mismatches: 23, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
20 114 0.61
21 44 0.24
22 28 0.15
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:1210273 original size:42 final size:41
Alignment explanation
Indices: 1210186--1210476 Score: 288
Period size: 42 Copynumber: 7.0 Consensus size: 41
1210176 ATTCGCGTTG
* * *
1210186 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCT-ACAGTTGCGTTGCGATTTTC
1210227 CATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCTACAGTTG-CGTTGCGATTTTC
* * * * *
1210269 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGATAGTCT-ACAGTTGCGTTGCGAT-TTTC
* ** ** *
1210311 AAAATCGCGTTGCGATTTTCT--ATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCTACAGTT-GCGTTGCGATTTTC
* * *
1210351 CATTTCGCGTTGCGAT--TTTCCATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCTACAGTT-GCGTTGCGATTTTC
*
1210391 CATTTCGCGTTGCGATAGTCTACAGTCGTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTCTACAGTTG-CGTTGCGATTTTC
* *
1210433 CATTTCGCGTTGCGATAATCTACAGTTGTCGTTGCAATTTTC
1 CATTTCGCGTTGCGATAGTCTACAGTTG-CGTTGCGATTTTC
1210475 CA
1 CA
1210477 AATTCTTTGC
Statistics
Matches: 211, Mismatches: 28, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
40 52 0.25
41 44 0.21
42 112 0.53
43 1 0.00
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.39
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTCTACAGTTGCGTTGCGATTTTC
Found at i:1210426 original size:22 final size:21
Alignment explanation
Indices: 1210398--1210467 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
1210388 TTCCATTTCG
1210398 CGTTGCGATAGTCTACAGTCGT
1 CGTTGCGATA-TCTACAGTCGT
* * *
1210420 CGTTGCGAT-TTTCCATTTCG-
1 CGTTGCGATATCTACA-GTCGT
*
1210440 CGTTGCGATAATCTACAGTTGT
1 CGTTGCGAT-ATCTACAGTCGT
1210462 CGTTGC
1 CGTTGC
1210468 AATTTTCCAA
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
20 13 0.35
21 5 0.14
22 19 0.51
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.37
Consensus pattern (21 bp):
CGTTGCGATATCTACAGTCGT
Found at i:1210432 original size:102 final size:102
Alignment explanation
Indices: 1210189--1210511 Score: 399
Period size: 102 Copynumber: 3.2 Consensus size: 102
1210179 CGCGTTGCAT
1210189 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATA-TCTACAGTT
* **
1210254 GTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
65 GTCGTTGCGATTTTCCATTTCGCGTTGCGAT-TTTCCAA
* * * * *
1210293 ATCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCTATTTCGCGTTGCGAT-TTTCCATTTC
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATATCTACAGTT-
*
1210357 G-CGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAT
65 GTCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAA
* *
1210394 TTCGCGTTGCGATAGTCT-ACAGTCGTCGTTGCGATTTTCCATTTCGCGTTGCGATAATCTACAG
1 TTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCCATTTCGCGTTGCGAT-ATCTACAG
* * *
1210458 TTGTCGTTGCAATTTTCCAAATT--CTTTGCGATTTTCCAAA
63 TTGTCGTTGCGATTTTCC-ATTTCGCGTTGCGATTTTCC-AA
1210498 TT--CGTTGCGATAGT
1 TTCGCGTTGCGATAGT
1210512 CTACAGTTGT
Statistics
Matches: 191, Mismatches: 20, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
101 23 0.12
102 76 0.40
103 15 0.08
104 74 0.39
105 3 0.02
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (102 bp):
TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATATCTACAGTTG
TCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAA
Found at i:1210491 original size:19 final size:19
Alignment explanation
Indices: 1210461--1210545 Score: 89
Period size: 19 Copynumber: 4.3 Consensus size: 19
1210451 TCTACAGTTG
*
1210461 TCGTTGCAATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
*
1210480 TCTTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
1210499 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
1210520 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
1210540 TCGTTG
1 TCGTTG
1210546 TGATAGTTAA
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
19 32 0.62
20 5 0.10
21 5 0.10
22 10 0.19
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:1210504 original size:122 final size:119
Alignment explanation
Indices: 1210255--1210508 Score: 264
Period size: 122 Copynumber: 2.1 Consensus size: 119
1210245 TCTACAGTTG
*
1210255 TCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTGAAAATCGCG
1 TCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTCAAAATCGCG
** * * * *
1210320 TTGCGATTTTCTATTTCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCATT
66 TTGCGATAATCTAGTTCGCGTTGCAATTTTCCAATTC-CGTTGCGATTTTCCAAT
* * * * **
1210375 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCT-ACAGTCGTCGTTGCGAT-TTTCCATTT
1 T--CGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATAGTTCAAAAT
*
1210438 CGCGTTGCGATAATCTACAGTT-GTCGTTGCAATTTTCCAAATT-CTTTGCGATTTTCCAAAT
62 CGCGTTGCGATAATCT--AGTTCG-CGTTGCAATTTTCC-AATTCCGTTGCGATTTTCC-AAT
1210499 TCGTTGCGAT
1 TCGTTGCGAT
1210509 AGTCTACAGT
Statistics
Matches: 111, Mismatches: 14, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
120 1 0.01
122 64 0.58
123 24 0.22
124 19 0.17
125 3 0.03
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.41
Consensus pattern (119 bp):
TCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTCAAAATCGCG
TTGCGATAATCTAGTTCGCGTTGCAATTTTCCAATTCCGTTGCGATTTTCCAAT
Found at i:1210515 original size:60 final size:60
Alignment explanation
Indices: 1210422--1210541 Score: 188
Period size: 60 Copynumber: 2.0 Consensus size: 60
1210412 ACAGTCGTCG
*
1210422 TTGCGATTTTCCATTTCGCGTTGCGATAATCTACAGTTGTCGTTGCAATTTTCCAAATTCT
1 TTGCGATTTTCCAATTC-CGTTGCGATAATCTACAGTTGTCGTTGCAATTTTCCAAATTCT
* *
1210483 TTGCGATTTTCCAAATT-CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTC
1 TTGCGATTTTCC-AATTCCGTTGCGATAATCTACAGTTGTCGTTGCAATTTTCCAAATTC
1210542 GTTGTGATAG
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
60 40 0.73
61 12 0.22
62 3 0.05
ACGTcount: A:0.20, C:0.21, G:0.17, T:0.42
Consensus pattern (60 bp):
TTGCGATTTTCCAATTCCGTTGCGATAATCTACAGTTGTCGTTGCAATTTTCCAAATTCT
Found at i:1210528 original size:164 final size:163
Alignment explanation
Indices: 1210211--1210536 Score: 410
Period size: 164 Copynumber: 2.0 Consensus size: 163
1210201 TAGTTGAAAA
*
1210211 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCATTTCG
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGTCGTTGCGATTTTCCATTTCG
* * * * *
1210276 CGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCTATTTCGCGT
66 CGTTGCGATAATTGAAAATCGCGTTGCAATAGTTCAAAATCGCGTTGCGATTTTCAAATTC-CGT
* * *
1210341 TGCGATTTTCCATTTCGCGTTGCGATTTTCCATT
130 TGCGATTCTACAGTTCGCGTTGCGATTTTCCATT
1210375 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGTCGTTGCGATTTTCCATTTCG
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGTCGTTGCGATTTTCCATTTCG
* * * * * * *
1210440 CGTTGCGATAATCT-ACAGTTGTCGTTGCAAT-TTTCCAAAT-TCTTTGCGATTTTCCAAATT-C
66 CGTTGCGATAAT-TGAAAATCG-CGTTGCAATAGTTCAAAATCGCGTTGCGATTTT-CAAATTCC
1210501 GTTGCGATAGTCTACAGTT-GTCGTTGCGATTTTCCA
128 GTTGCGAT--TCTACAGTTCG-CGTTGCGATTTTCCA
1210537 AATTCGTTGT
Statistics
Matches: 140, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
162 9 0.06
163 12 0.09
164 110 0.79
165 9 0.06
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (163 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGTCGTTGCGATTTTCCATTTCG
CGTTGCGATAATTGAAAATCGCGTTGCAATAGTTCAAAATCGCGTTGCGATTTTCAAATTCCGTT
GCGATTCTACAGTTCGCGTTGCGATTTTCCATT
Found at i:1210642 original size:6 final size:6
Alignment explanation
Indices: 1210631--1210686 Score: 105
Period size: 6 Copynumber: 9.5 Consensus size: 6
1210621 GACACGTATT
1210631 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1210679 ACC-CG ACC
1 ACCACG ACC
1210687 CGAGACGAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.10
6 45 0.90
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1211182 original size:5 final size:5
Alignment explanation
Indices: 1211168--1211208 Score: 75
Period size: 5 Copynumber: 8.4 Consensus size: 5
1211158 CCGCCGCCGC
1211168 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CG
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CG
1211209 GGTCGGGTCG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.11
5 32 0.89
ACGTcount: A:0.00, C:0.41, G:0.22, T:0.37
Consensus pattern (5 bp):
CGTCT
Found at i:1211240 original size:6 final size:6
Alignment explanation
Indices: 1211209--1211267 Score: 90
Period size: 6 Copynumber: 10.5 Consensus size: 6
1211199 TCTCGTCTCG
1211209 GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1211253 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
1211268 AATGGTAATG
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 20 0.38
6 33 0.62
ACGTcount: A:0.00, C:0.17, G:0.54, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:1211273 original size:6 final size:6
Alignment explanation
Indices: 1211264--1211300 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
1211254 GTCGTGGTCG
1211264 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA T
1 TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA TGGTAA T
1211301 ACGTGTCTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (6 bp):
TGGTAA
Found at i:1211273 original size:12 final size:12
Alignment explanation
Indices: 1211234--1211297 Score: 56
Period size: 12 Copynumber: 5.3 Consensus size: 12
1211224 GGTCGGGTCG
**
1211234 TGGTCGTGGTCG
1 TGGTCGTGGTAA
**
1211246 TGGTCGTGGTCG
1 TGGTCGTGGTAA
1211258 TGGTCGTGGTAA
1 TGGTCGTGGTAA
**
1211270 TGGTAATGGTAA
1 TGGTCGTGGTAA
**
1211282 TGGTAATGGTAA
1 TGGTCGTGGTAA
1211294 TGGT
1 TGGT
1211298 AATACGTGTC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 48 1.00
ACGTcount: A:0.16, C:0.08, G:0.42, T:0.34
Consensus pattern (12 bp):
TGGTCGTGGTAA
Found at i:1211273 original size:18 final size:18
Alignment explanation
Indices: 1211234--1211273 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1211224 GGTCGGGTCG
**
1211234 TGGTCGTGGTCGTGGTCG
1 TGGTCGTGGTCGTGGTAA
1211252 TGGTCGTGGTCGTGGTAA
1 TGGTCGTGGTCGTGGTAA
1211270 TGGT
1 TGGT
1211274 AATGGTAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.05, C:0.12, G:0.47, T:0.35
Consensus pattern (18 bp):
TGGTCGTGGTCGTGGTAA
Found at i:1211870 original size:53 final size:50
Alignment explanation
Indices: 1211793--1211928 Score: 156
Period size: 47 Copynumber: 2.8 Consensus size: 50
1211783 AATATAATAT
* *
1211793 AAACT-TATACTAATATAAATTATATGATATATATATATATATATATGTATCA
1 AAACTATATAATAATATAAACTATAT-ATATATATATATATATATA--TATCA
* *
1211845 AAGCTATATATTAATATAAAC--TATATATA-ATATATATATATATATCA
1 AAACTATATAATAATATAAACTATATATATATATATATATATATATATCA
* *
1211892 AAATTATATAATAATATAAACTATATA-ATATGTATAT
1 AAACTATATAATAATATAAACTATATATATATATATAT
1211929 CAAAACTACA
Statistics
Matches: 73, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
47 23 0.32
48 3 0.04
49 22 0.30
50 5 0.07
51 3 0.04
52 4 0.05
53 13 0.18
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (50 bp):
AAACTATATAATAATATAAACTATATATATATATATATATATATATATCA
Found at i:1211881 original size:47 final size:48
Alignment explanation
Indices: 1211819--1211928 Score: 161
Period size: 47 Copynumber: 2.3 Consensus size: 48
1211809 AAATTATATG
* * *
1211819 ATATATATATATATATATATGTATCAAAGCTATATATTAATATAAACT
1 ATATATATATATATATATATATATCAAAACTATATAATAATATAAACT
*
1211867 ATATATA-ATATATATATATATATCAAAATTATATAATAATATAAACT
1 ATATATATATATATATATATATATCAAAACTATATAATAATATAAACT
*
1211914 ATATA-ATATGTATAT
1 ATATATATATATATAT
1211929 CAAAACTACA
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
46 1 0.02
47 48 0.86
48 7 0.12
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.42
Consensus pattern (48 bp):
ATATATATATATATATATATATATCAAAACTATATAATAATATAAACT
Found at i:1211901 original size:2 final size:2
Alignment explanation
Indices: 1211813--1211889 Score: 61
Period size: 2 Copynumber: 38.5 Consensus size: 2
1211803 TAATATAAAT
* * **
1211813 TA TA TGA TA TA TA TA TA TA TA TA TA TG TA TCA AA GC TA TA TA T-
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
*
1211856 TA -A TA TA AA CTA TA TA TA -A 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 T
1211890 CAAAATTATA
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
1 3 0.05
2 53 0.88
3 4 0.07
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1211919 original size:17 final size:17
Alignment explanation
Indices: 1211786--1211921 Score: 99
Period size: 16 Copynumber: 8.2 Consensus size: 17
1211776 TATTTGAAAT
1211786 ATAATATAAACT-TATA
1 ATAATATAAACTATATA
* * *
1211802 CTAATATAAATTATATG
1 ATAATATAAACTATATA
*
1211819 AT-ATATATA-TATATA
1 ATAATATAAACTATATA
*
1211834 TATATGTATCAAAGCTATATA
1 -ATA-ATAT-AAA-CTATATA
*
1211855 TTAATATAAACTATAT-
1 ATAATATAAACTATATA
*
1211871 ATAATATATA-TATAT-
1 ATAATATAAACTATATA
*
1211886 AT-ATCA-AAATTATATA
1 ATAAT-ATAAACTATATA
1211902 ATAATATAAACTATATA
1 ATAATATAAACTATATA
1211919 ATA
1 ATA
1211922 TGTATATCAA
Statistics
Matches: 94, Mismatches: 14, Indels: 23
0.72 0.11 0.18
Matches are distributed among these distances:
14 4 0.04
15 18 0.19
16 29 0.31
17 24 0.26
18 6 0.06
19 5 0.05
20 2 0.02
21 6 0.06
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.40
Consensus pattern (17 bp):
ATAATATAAACTATATA
Found at i:1211928 original size:39 final size:40
Alignment explanation
Indices: 1211874--1211950 Score: 111
Period size: 39 Copynumber: 1.9 Consensus size: 40
1211864 ACTATATATA
* *
1211874 ATATATATATATATATCAAAATTATATAATAATATAAACT
1 ATATATATATATATATCAAAACTACATAATAATATAAACT
* *
1211914 ATATA-ATATGTATATCAAAACTACATACTAATATAAA
1 ATATATATATATATATCAAAACTACATAATAATATAAA
1211951 TTATTCCCTC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
39 28 0.85
40 5 0.15
ACGTcount: A:0.55, C:0.08, G:0.01, T:0.36
Consensus pattern (40 bp):
ATATATATATATATATCAAAACTACATAATAATATAAACT
Done.