Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001497.1 Hibiscus syriacus cultivar Beakdansim tig00002919_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: 1780709
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 4 of 8
Found at i:673224 original size:10 final size:10
Alignment explanation
Indices: 673192--673235 Score: 52
Period size: 10 Copynumber: 4.1 Consensus size: 10
673182 GTGTTTGTGT
673192 TGTTCGTTTA
1 TGTTCGTTTA
*
673202 TGTTCCTTTTTTA
1 TGTT-C--GTTTA
673215 TGTTCGTTTA
1 TGTTCGTTTA
673225 TGTTCGTTTA
1 TGTTCGTTTA
673235 T
1 T
673236 CATTTAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
10 19 0.66
11 1 0.03
12 1 0.03
13 8 0.28
ACGTcount: A:0.09, C:0.11, G:0.16, T:0.64
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:674381 original size:2 final size:2
Alignment explanation
Indices: 674374--674427 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
674364 CTCTTTAATT
674374 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
674416 TA TA TA TA TA TA
1 TA TA TA TA TA TA
674428 ACAGATATAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:675750 original size:17 final size:16
Alignment explanation
Indices: 675719--675753 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
675709 TTAATATAAG
675719 TTTTAGAAATATAATT
1 TTTTAGAAATATAATT
*
675735 TTTTATGAATTATAATT
1 TTTTA-GAAATATAATT
675752 TT
1 TT
675754 ATCTCATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (16 bp):
TTTTAGAAATATAATT
Found at i:675755 original size:15 final size:16
Alignment explanation
Indices: 675711--675753 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
675701 TTTTGTATTT
*
675711 AATATAAGTTTTA-GA
1 AATATAATTTTTATGA
675726 AATATAATTTTTTATGA
1 AATATAA-TTTTTATGA
*
675743 ATTATAATTTT
1 AATATAATTTT
675754 ATCTCATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.29
16 9 0.38
17 8 0.33
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (16 bp):
AATATAATTTTTATGA
Found at i:688275 original size:19 final size:18
Alignment explanation
Indices: 688247--688282 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
688237 AATATGACAC
*
688247 AAAGATAAAAGTTTTATA
1 AAAGATAAAACTTTTATA
688265 AAAGCATAAAACTTTTAT
1 AAAG-ATAAAACTTTTAT
688283 CTTTGAAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.33
Consensus pattern (18 bp):
AAAGATAAAACTTTTATA
Found at i:688747 original size:2 final size:2
Alignment explanation
Indices: 688740--688773 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
688730 TTTTAATCCG
688740 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
688774 TTGGCAATCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:692279 original size:17 final size:16
Alignment explanation
Indices: 692257--692310 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
692247 TAATGTTAAT
692257 ATTTAAATTTATTTTTA
1 ATTTAAA-TTATTTTTA
* *
692274 ATTTAAAGTTATTATGA
1 ATTTAAA-TTATTTTTA
* *
692291 ATTTATATTAATTTTA
1 ATTTAAATTATTTTTA
692307 ATTT
1 ATTT
692311 TTTATAATGT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 10 0.33
17 20 0.67
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (16 bp):
ATTTAAATTATTTTTA
Found at i:693807 original size:34 final size:34
Alignment explanation
Indices: 693749--693845 Score: 124
Period size: 34 Copynumber: 2.8 Consensus size: 34
693739 ATGTTTTTAG
* *
693749 AATACAAATTATATTATTCAAAATTTAAAATAAA
1 AATAAAAATTATATTATTCGAAATTTAAAATAAA
* *
693783 AATAAAAATAATATTATTCGAAATTTAAAATTAA
1 AATAAAAATTATATTATTCGAAATTTAAAATAAA
*
693817 AATATAAATTATATTAAGTT-GAAATTTAA
1 AATAAAAATTATATT-A-TTCGAAATTTAA
693846 CATTAAATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
34 43 0.78
35 10 0.18
36 2 0.04
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (34 bp):
AATAAAAATTATATTATTCGAAATTTAAAATAAA
Found at i:694642 original size:128 final size:128
Alignment explanation
Indices: 694248--694853 Score: 1043
Period size: 128 Copynumber: 4.7 Consensus size: 128
694238 ACAATCCATC
*
694248 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTATCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * *
694313 AGAAGGTGCGCCCCCGGGAACGCGCCTTCAAGTCCCTTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
* *
694376 TAGTGTACCTGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * * *
694441 GAAAGGCGC-CCCCCGAGAACGCACCTTCAAGTCCCCTGAGAAATAATAGGTTCTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
694503 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
694568 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTTCTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
*
694631 TAGTGTCCCCGAGGGACATGAGTAACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* *
694696 GGAAGGCGCGACCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTTATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
* ***
694759 TAGTATCCGTAAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
694824 GGAAGGCGCGCCCCCGGGAACGCGCCTTCA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCA
694854 TGTGAATAGT
Statistics
Matches: 452, Mismatches: 25, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
127 120 0.27
128 332 0.73
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (128 bp):
TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
Found at i:694704 original size:255 final size:256
Alignment explanation
Indices: 694248--694853 Score: 1043
Period size: 255 Copynumber: 2.4 Consensus size: 256
694238 ACAATCCATC
*
694248 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTATCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * *
694313 AGAAGGTGCGCCCCCGGGAACGCGCCTTCAAGTCCCTTGAGAAATAATAGGTACTGATATGAATA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATA
* *
694378 GTGTACCTGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGA
131 GTGTACCCGAGGGACATGAGTAACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGA
* *
694443 AAGGCGC-CCCCCGAGAACGCACCTTCAAGTCCCCTGAGAAATAATAGGTTCTGATATGAA
196 AAGGCGCGACCCCGAGAACGCACCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
694503 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
694568 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTTCTGATATGAATA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATA
* *
694633 GTGTCCCCGAGGGACATGAGTAACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGG
131 GTGTACCCGAGGGACATGAGTAACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGA
* * *
694698 AAGGCGCGACCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTTATATGAA
196 AAGGCGCGACCCCGAGAACGCACCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
* ***
694759 TAGTATCCGTAAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
694824 GGAAGGCGCGCCCCCGGGAACGCGCCTTCA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCA
694854 TGTGAATAGT
Statistics
Matches: 332, Mismatches: 18, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
255 193 0.58
256 139 0.42
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (256 bp):
TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAATA
GTGTACCCGAGGGACATGAGTAACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGA
AAGGCGCGACCCCGAGAACGCACCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
Found at i:694947 original size:8 final size:8
Alignment explanation
Indices: 694934--694974 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
694924 TCACAAGCTT
694934 TCAAATTC
1 TCAAATTC
694942 TCAAATTC
1 TCAAATTC
* *
694950 CCAAACTC
1 TCAAATTC
694958 T-AAATTC
1 TCAAATTC
694965 TCAAATTC
1 TCAAATTC
694973 TC
1 TC
694975 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:711502 original size:3 final size:3
Alignment explanation
Indices: 711494--711544 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
711484 TACTTTACCC
711494 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
711542 TAA
1 TAA
711545 ATCAACCTGC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:726772 original size:35 final size:35
Alignment explanation
Indices: 726733--726802 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
726723 AAAACAATCC
* ** *
726733 TCAATTTCATTCTAAACCTTAAATTCTAAAATAAT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATAAT
726768 TCAATTACATTCTAAACCCCAAATTCCAAAATAAT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATAAT
726803 CAAAATAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.34
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAATTCCAAAATAAT
Found at i:739107 original size:16 final size:17
Alignment explanation
Indices: 739079--739113 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
739069 CTTGTTCAAC
739079 ATAAATCACAGTGACAA
1 ATAAATCACAGTGACAA
*
739096 ATAAAT-ACAGTGATAA
1 ATAAATCACAGTGACAA
739112 AT
1 AT
739114 TAAGTAATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.23
Consensus pattern (17 bp):
ATAAATCACAGTGACAA
Found at i:740233 original size:2 final size:2
Alignment explanation
Indices: 740226--740262 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
740216 AATAAATAGT
740226 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
740263 GTGTGTGTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:740267 original size:2 final size:2
Alignment explanation
Indices: 740262--740289 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
740252 TATATATATA
740262 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
740290 GTTTTAGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:741698 original size:133 final size:130
Alignment explanation
Indices: 741436--741711 Score: 400
Period size: 133 Copynumber: 2.1 Consensus size: 130
741426 ACATATACAC
741436 TAATTATTATATAAAATGACAATATAAATAAAGTAAAATATAAATAAACTATATACTAATGAATA
1 TAATTATTATATAAAATGACAATATAAATAAAGTAAAATATAAATAAACTATATACTAATGAATA
* * ** *
741501 TACAATATATTGATTTTAATTTTGTTCAGATATTAACAAAATCAATTTTAAATCGACAAATATAT
66 TACAATATATTGATTTTAATTTTGTTCAGATAGTAAAAAAAAAAATTTAAAATCGACAAATATAT
741566 TAATTATTATATAAAATGACAATATAAATAAAGTAATAA-ATAAATAAATCTATATACTAATGAA
1 TAATTATTATATAAAATGACAATATAAATAAAGTAA-AATATAAATAAA-CTATATACTAATGAA
** *
741630 TATACATAATATATTGATTTTAATTTTGTTTTG-TCAGTAAAAAAAAAAATTTAAAATCGACAAC
64 TATAC--AATATATTGATTTTAATTTTGTTCAGAT-AGTAAAAAAAAAAATTTAAAATCGACAAA
741694 TATAT
126 TATAT
741699 T-ATTA-TATA-AAAA
1 TAATTATTATATAAAA
741712 GGGGAAAGTG
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
130 49 0.37
131 26 0.20
132 5 0.04
133 53 0.40
ACGTcount: A:0.51, C:0.06, G:0.05, T:0.37
Consensus pattern (130 bp):
TAATTATTATATAAAATGACAATATAAATAAAGTAAAATATAAATAAACTATATACTAATGAATA
TACAATATATTGATTTTAATTTTGTTCAGATAGTAAAAAAAAAAATTTAAAATCGACAAATATAT
Found at i:742193 original size:72 final size:72
Alignment explanation
Indices: 742093--742240 Score: 278
Period size: 72 Copynumber: 2.1 Consensus size: 72
742083 GTATTGTGTG
742093 TAAGAAAGAACCGGAATCAATAAATCATTTACTCTGTCATTGTGAGCACGCATGGATCTACTTGT
1 TAAGAAAGAACCGGAATCAATAAATCATTTACTCTGTCATTGTGAGCACGCATGGATCTACTTGT
742158 TGAATGA
66 TGAATGA
*
742165 TAAGAAAGAACCGGAATCAATAAATCATTTACTCTGTCATTGTGAGCATGCATGGATCTACTTGT
1 TAAGAAAGAACCGGAATCAATAAATCATTTACTCTGTCATTGTGAGCACGCATGGATCTACTTGT
*
742230 TGAATGC
66 TGAATGA
742237 TAAG
1 TAAG
742241 TCACAAGCTA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (72 bp):
TAAGAAAGAACCGGAATCAATAAATCATTTACTCTGTCATTGTGAGCACGCATGGATCTACTTGT
TGAATGA
Found at i:747149 original size:23 final size:22
Alignment explanation
Indices: 747108--747156 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
747098 ACATTAATTA
747108 AATTTAATTATTATATTTTGAATC
1 AATTTAATTATTATATTTT--ATC
747132 AATTT-ATTATTA-ACTTTTATC
1 AATTTAATTATTATA-TTTTATC
747153 AATT
1 AATT
747157 AATCATAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 7 0.29
22 1 0.04
23 11 0.46
24 5 0.21
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55
Consensus pattern (22 bp):
AATTTAATTATTATATTTTATC
Found at i:753671 original size:186 final size:184
Alignment explanation
Indices: 753435--753824 Score: 656
Period size: 186 Copynumber: 2.1 Consensus size: 184
753425 TTAAAATATT
* * *
753435 AAATATTAAATATATTATATATAGCATATGGGTTCAGCCCAAACCATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGTTCAACCCAAACCATTTAAAACCCAATTAATAA
753500 TTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATT-AAAAATTTATATAAAATTT
* * *
753565 TTATTTTATAATTATATATTATTTAAATTATTTGTAAATTATTTTTCTGAATTAAA
130 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTT-TGAATTAAA
*
753621 AAATATTAAATATATTATATATAACATATGGGTTCAACCCAAATCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGTTCAACCCAAACCATTTAAAACCCAATTAATAA
753686 TTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAATTTATATAAAATTTT
66 TTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAATTTATATAAAATTTT
* *
753751 TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTGAATTATA
131 TATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTGAATTAAA
* *
753805 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
753825 AATTAGAAAA
Statistics
Matches: 193, Mismatches: 11, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
183 8 0.04
184 18 0.09
185 61 0.32
186 106 0.55
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.43
Consensus pattern (184 bp):
AAATATTAAATATATTATATATAACATATGGGTTCAACCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAATTTATATAAAATTTT
TATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTGAATTAAA
Found at i:755650 original size:23 final size:23
Alignment explanation
Indices: 755615--755660 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
755605 TACATGCCAT
755615 TGGTGTTATTAATATTATATTTA
1 TGGTGTTATTAATATTATATTTA
*
755638 TGGTG-TATCTAATATTATTTTTA
1 TGGTGTTAT-TAATATTATATTTA
755661 GAACATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.28, C:0.02, G:0.13, T:0.57
Consensus pattern (23 bp):
TGGTGTTATTAATATTATATTTA
Found at i:760829 original size:21 final size:22
Alignment explanation
Indices: 760800--760873 Score: 82
Period size: 21 Copynumber: 3.5 Consensus size: 22
760790 GCGGAAAATA
* *
760800 GAATGCGGGGAATG-CGGCATC
1 GAATCCGGGGAATGAAGGCATC
**
760821 GAATCCGGGG-ATGAATCCATC
1 GAATCCGGGGAATGAAGGCATC
*
760842 GAATCCGGGGAA-GATGGCATC
1 GAATCCGGGGAATGAAGGCATC
760863 GAATCCGGGGA
1 GAATCCGGGGA
760874 TGACGTCGAT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 3 0.07
21 40 0.91
22 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.38, T:0.15
Consensus pattern (22 bp):
GAATCCGGGGAATGAAGGCATC
Found at i:762021 original size:56 final size:57
Alignment explanation
Indices: 761957--762480 Score: 400
Period size: 56 Copynumber: 9.3 Consensus size: 57
761947 GATCATTTCA
*
761957 TTTCTTTAATATTAAGCGATGACAATAATATTTTTTAGTTGATCACTGATCGTTTTG
1 TTTCTTTAATATTAAGCGATGATAATAATATTTTTTAGTTGATCACTGATCGTTTTG
* * ** * * * **
762014 ATT-TTTAATATTAAGCAATGATAACGGA-ATTTTTTAGTTGATTA-TCAATTGTTTCA
1 TTTCTTTAATATTAAGCGATGATAA-TAATATTTTTTAGTTGATCACT-GATCGTTTTG
* * ** * * * * * *
762070 TTTCTTTAATATTAAGCGGTGAT-TTCGGTA-CTTTTAGTTAACCACTTACCGTTTTA
1 TTTCTTTAATATTAAGCGATGATAAT-AATATTTTTTAGTTGATCACTGATCGTTTTG
* * * * * *
762126 TTTCTTTAATATTAAACGGTGTTAATAGTGTTTTTTAGTTGATCACTGATCCTTTTG
1 TTTCTTTAATATTAAGCGATGATAATAATATTTTTTAGTTGATCACTGATCGTTTTG
* * * * * *
762183 TTTCTTTAATATTAAACGATGACAATAGTGTTTTTTAGTTGATCAATGATCATTTTG
1 TTTCTTTAATATTAAGCGATGATAATAATATTTTTTAGTTGATCACTGATCGTTTTG
* * * *
762240 TTTCTTTAATACTAAGCAATGACAACT-ATGTTTTTTAGTTGATCACTGATCGTTTTG
1 TTTCTTTAATATTAAGCGATGATAA-TAATATTTTTTAGTTGATCACTGATCGTTTTG
* * * * * *
762297 TTTCTTTAATATTAAGTGGTGATAGTGAT-TTTTTTAGTTGATCACCGATCGTTTCG
1 TTTCTTTAATATTAAGCGATGATAATAATATTTTTTAGTTGATCACTGATCGTTTTG
* ** * * * * *
762353 TTTCTTTAATATTAAGCGGTGATGTTAAT-GTTTTTAATTGATCACCGATCATTTCG
1 TTTCTTTAATATTAAGCGATGATAATAATATTTTTTAGTTGATCACTGATCGTTTTG
** * * ** * * * * *
762409 TTTCTTTAATATTAAATGGTGATGATGGTA-TTTTTAATTAATCAATGATCATTTCG
1 TTTCTTTAATATTAAGCGATGATAATAATATTTTTTAGTTGATCACTGATCGTTTTG
762465 TTTCTTTAATATTAAG
1 TTTCTTTAATATTAAG
762481 AGGTTATATC
Statistics
Matches: 385, Mismatches: 71, Indels: 23
0.80 0.15 0.05
Matches are distributed among these distances:
55 1 0.00
56 219 0.57
57 164 0.43
58 1 0.00
ACGTcount: A:0.27, C:0.11, G:0.15, T:0.48
Consensus pattern (57 bp):
TTTCTTTAATATTAAGCGATGATAATAATATTTTTTAGTTGATCACTGATCGTTTTG
Found at i:762058 original size:113 final size:113
Alignment explanation
Indices: 761947--762423 Score: 365
Period size: 113 Copynumber: 4.2 Consensus size: 113
761937 AATGATTATG
*
761947 GATCATTTCATTTCTTTAATATTAAGCGATGACAATAATATTTTTTAGTTGATCACTGATCGTTT
1 GATCGTTTCATTTCTTTAATATTAAGCGATGACAATAATATTTTTTAGTTGATCACTGATCGTTT
*
762012 TGATT-TTTAATATTAAGCAATGATAACGGAATTTTTTAGTTGATTA-T
66 TGATTCTTTAATATTAAGCAATGATAAC-GAATTTTTTAGTTGATCACT
* * * ** ** * * * * *
762059 CAATTGTTTCATTTCTTTAATATTAAGCGGTGA-TTTCGGTA-CTTTTAGTTAACCACTTACCGT
1 -GATCGTTTCATTTCTTTAATATTAAGCGATGACAAT-AATATTTTTTAGTTGATCACTGATCGT
* ** * * **
762122 TTT-ATTTCTTTAATATTAAACGGTGTTAATAGTGTTTTTTAGTTGATCACT
64 TTTGA-TTCTTTAATATTAAGCAATGATAA-CGAATTTTTTAGTTGATCACT
* ** * * * * *
762173 GATCCTTTTGTTTCTTTAATATTAAACGATGACAATAGTGTTTTTTAGTTGATCAATGATCATTT
1 GATCGTTTCATTTCTTTAATATTAAGCGATGACAATAATATTTTTTAGTTGATCACTGATCGTTT
* * * * *
762238 TGTTTCTTTAATACTAAGCAATGACAACTATGTTTTTTAGTTGATCACT
66 TGATTCTTTAATATTAAGCAATGATAACGA-ATTTTTTAGTTGATCACT
** * * * * * *
762287 GATCGTTTTGTTTCTTTAATATTAAGTGGTGATAGTGAT-TTTTTTAGTTGATCACCGATCGTTT
1 GATCGTTTCATTTCTTTAATATTAAGCGATGACAATAATATTTTTTAGTTGATCACTGATCGTTT
* * ** *** * *
762351 CGTTTCTTTAATATTAAGCGGTGAT-GTTAATGTTTTTAATTGATCACC
66 TGATTCTTTAATATTAAGCAATGATAACGAAT-TTTTTAGTTGATCACT
* *
762399 GATCATTTCGTTTCTTTAATATTAA
1 GATCGTTTCATTTCTTTAATATTAA
762424 ATGGTGATGA
Statistics
Matches: 282, Mismatches: 72, Indels: 21
0.75 0.19 0.06
Matches are distributed among these distances:
111 2 0.01
112 62 0.22
113 131 0.46
114 87 0.31
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (113 bp):
GATCGTTTCATTTCTTTAATATTAAGCGATGACAATAATATTTTTTAGTTGATCACTGATCGTTT
TGATTCTTTAATATTAAGCAATGATAACGAATTTTTTAGTTGATCACT
Found at i:762085 original size:57 final size:58
Alignment explanation
Indices: 761952--762369 Score: 225
Period size: 57 Copynumber: 7.4 Consensus size: 58
761942 TTATGGATCA
* * *
761952 TTTCATTTCTTTAATATTAAGCGATGACAATAATATTTTTTAGTTGATCACTGATCGT
1 TTTCATTTCTTTAATATTAAGCAATGACAAGAATATTTTTTAGTTGATCACTAATCGT
* * * * *
762010 TTTGA-TT-TTTAATATTAAGCAATGATAACGGA-ATTTTTTAGTTGATTA-TCAATTG-
1 TTTCATTTCTTTAATATTAAGCAATGACAA-GAATATTTTTTAGTTGATCACT-AATCGT
** *** * * * * * *
762065 TTTCATTTCTTTAATATTAAGCGGTGATTTCG-GTA-CTTTTAGTTAACCACTTACCGT
1 TTTCATTTCTTTAATATTAAGCAATGA-CAAGAATATTTTTTAGTTGATCACTAATCGT
* ** ** * * * * *
762122 TTT-ATTTCTTTAATATTAAACGGTGTTAATAGTGTTTTTTAGTTGATCACTGATCCT
1 TTTCATTTCTTTAATATTAAGCAATGACAAGAATATTTTTTAGTTGATCACTAATCGT
* * * * * * * * *
762179 TTT-GTTTCTTTAATATTAAACGATGACAATAGTGTTTTTTAGTTGATCAATGATCAT
1 TTTCATTTCTTTAATATTAAGCAATGACAAGAATATTTTTTAGTTGATCACTAATCGT
* * ** * *
762236 TTT-GTTTCTTTAATACTAAGCAATGACAACTATGTTTTTTAGTTGATCACTGATCGT
1 TTTCATTTCTTTAATATTAAGCAATGACAAGAATATTTTTTAGTTGATCACTAATCGT
* *** * * **
762293 TTT-GTTTCTTTAATATTAAGTGGTGA-TAGTGAT-TTTTTTAGTTGATCACCGATCG-
1 TTTCATTTCTTTAATATTAAGCAATGACAAG-AATATTTTTTAGTTGATCACTAATCGT
*
762348 TTTCGTTTCTTTAATATTAAGC
1 TTTCATTTCTTTAATATTAAGC
762370 GGTGATGTTA
Statistics
Matches: 292, Mismatches: 56, Indels: 26
0.78 0.15 0.07
Matches are distributed among these distances:
55 9 0.03
56 113 0.39
57 165 0.57
58 5 0.02
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (58 bp):
TTTCATTTCTTTAATATTAAGCAATGACAAGAATATTTTTTAGTTGATCACTAATCGT
Found at i:762241 original size:27 final size:28
Alignment explanation
Indices: 762154--762304 Score: 78
Period size: 27 Copynumber: 5.4 Consensus size: 28
762144 GTGTTAATAG
* *
762154 TGTTT-TTTAGTTGATCACTGATCCTTT
1 TGTTTCTTTAGTTGATCAATGATCATTT
* * * * **
762181 TGTTTCTTTAATATTAAACGATGA-CAATAG
1 TGTTTCTTT-A-GTTGATCAATGATC-ATTT
762211 TGTTT-TTTAGTTGATCAATGATCATTT
1 TGTTTCTTTAGTTGATCAATGATCATTT
* * * * *
762238 TGTTTCTTTAATACTAAGCAATGA-CAACTA
1 TGTTTCTTTAGT--TGATCAATGATC-ATTT
* *
762268 TGTTT-TTTAGTTGATCACTGATCGTTT
1 TGTTTCTTTAGTTGATCAATGATCATTT
762295 TGTTTCTTTA
1 TGTTTCTTTA
762305 ATATTAAGTG
Statistics
Matches: 87, Mismatches: 26, Indels: 21
0.65 0.19 0.16
Matches are distributed among these distances:
27 33 0.38
28 15 0.17
29 11 0.13
30 28 0.32
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.50
Consensus pattern (28 bp):
TGTTTCTTTAGTTGATCAATGATCATTT
Found at i:762666 original size:57 final size:57
Alignment explanation
Indices: 762595--762722 Score: 170
Period size: 57 Copynumber: 2.2 Consensus size: 57
762585 TAACAGTGTT
* * * *
762595 TTTTTAATTTATCACTGATTGTTT-AGTTTCTTTAATATTGAGC-GACGACAGTGGTGC
1 TTTTTAATTGATCACTGATTGTTTCA-TTTCTCTAATATTAAGCAG-CGACAGCGGTGC
*
762652 TTTTTAATTGATCACTGATTGTTTCATTTCTCTAATATTAAGCAGTGACAGCGGTGC
1 TTTTTAATTGATCACTGATTGTTTCATTTCTCTAATATTAAGCAGCGACAGCGGTGC
*
762709 TTTTTAGTTGATCA
1 TTTTTAATTGATCA
762723 TCGACCGTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
57 61 0.97
58 2 0.03
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.45
Consensus pattern (57 bp):
TTTTTAATTGATCACTGATTGTTTCATTTCTCTAATATTAAGCAGCGACAGCGGTGC
Found at i:762733 original size:57 final size:55
Alignment explanation
Indices: 762625--762844 Score: 179
Period size: 57 Copynumber: 4.1 Consensus size: 55
762615 GTTTAGTTTC
* ** * **
762625 TTTAATATTGAGCGACGACAGTGGTGCTTTTTAATTGATCA-CTGATTGTTTCATT
1 TTTAATATTAAGCGGTGACAGTGGTGCTTTTTAGTTGATCATC-GACCGTTTCATT
* *
762680 TCTCTAATATTAAGCAGTGACAGCGGTGCTTTTTAGTTGATCATCGACCGTTTC---
1 T-T-TAATATTAAGCGGTGACAGTGGTGCTTTTTAGTTGATCATCGACCGTTTCATT
* * * * *
762734 TTTAATATT-ATCTGGTGACAGTAGTG-TTTTT--TT-AGCACCGACAGTTTCATTT
1 TTTAATATTAAGC-GGTGACAGTGGTGCTTTTTAGTTGATCATCGACCGTTTCA-TT
* * *
762786 TTTAATATTTAAGCGGTGACAATTGTGCTTTTTAGTTGATCATCGACCATTTCATT
1 TTTAATA-TTAAGCGGTGACAGTGGTGCTTTTTAGTTGATCATCGACCGTTTCATT
762842 TTT
1 TTT
762845 TTTTAGTGTT
Statistics
Matches: 129, Mismatches: 22, Indels: 27
0.72 0.12 0.15
Matches are distributed among these distances:
48 12 0.09
49 2 0.02
51 7 0.05
52 24 0.19
53 14 0.11
54 8 0.06
55 1 0.01
56 8 0.06
57 52 0.40
58 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.44
Consensus pattern (55 bp):
TTTAATATTAAGCGGTGACAGTGGTGCTTTTTAGTTGATCATCGACCGTTTCATT
Found at i:762913 original size:10 final size:11
Alignment explanation
Indices: 762894--762918 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
762884 TGAATGATCA
762894 TTTTATTTTTT
1 TTTTATTTTTT
762905 TTTTATTTTTT
1 TTTTATTTTTT
762916 TTT
1 TTT
762919 GTAATTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTATTTTTT
Found at i:763609 original size:16 final size:16
Alignment explanation
Indices: 763571--763614 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
763561 AAAAATAATG
*
763571 TGATTATATTATCCAA
1 TGATTACATTATCCAA
* * *
763587 CGGTTACATTATTCAA
1 TGATTACATTATCCAA
763603 TGATTACATTAT
1 TGATTACATTAT
763615 AAAATTATTA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (16 bp):
TGATTACATTATCCAA
Found at i:765708 original size:7 final size:7
Alignment explanation
Indices: 765696--765726 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
765686 TCAACTTCAT
765696 TATAATA
1 TATAATA
765703 TATAATA
1 TATAATA
765710 TATAATA
1 TATAATA
765717 TATAATA
1 TATAATA
765724 TAT
1 TAT
765727 TGTCATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
TATAATA
Found at i:774680 original size:219 final size:219
Alignment explanation
Indices: 774301--774738 Score: 858
Period size: 219 Copynumber: 2.0 Consensus size: 219
774291 TGTAGATAGC
774301 GCGGGCTCACTGGTGAAAAGAGGGTTACATCAGGCTCCCTTCCTAATGAGCTTTTACCCTTTCAG
1 GCGGGCTCACTGGTGAAAAGAGGGTTACATCAGGCTCCCTTCCTAATGAGCTTTTACCCTTTCAG
*
774366 ATTAGTAAACAACGATATCAAAATAGGCAGTCCTCTTTTACTCTTATTTCACCAGAAGCCAAACA
66 ATTAGTAAACAACGATATCAAAATAGGCAGTCCTCTTTTACTCTTATTTCACCAGAAACCAAACA
774431 CTCTAAAAATGAAGTAGCTATACAAATTCCTCACTTAATCCACAAAACTACATTAACCGATAACA
131 CTCTAAAAATGAAGTAGCTATACAAATTCCTCACTTAATCCACAAAACTACATTAACCGATAACA
774496 ATAGCTGTAATTCAAATAAATGGG
196 ATAGCTGTAATTCAAATAAATGGG
774520 GCGGGCTCACTGGTGAAAAGAGGGTTACATCAGGCTCCCTTCCTAATGAGCTTTTACCCTTTCAG
1 GCGGGCTCACTGGTGAAAAGAGGGTTACATCAGGCTCCCTTCCTAATGAGCTTTTACCCTTTCAG
774585 ATTAGTAAACAACGATATCAAAATAGGCAGTCCTCTTTTACTCTTATTTCACCAGAAACCAAACA
66 ATTAGTAAACAACGATATCAAAATAGGCAGTCCTCTTTTACTCTTATTTCACCAGAAACCAAACA
*
774650 CTCTAAAAATGAAGTAGCTCTACAAATTCCTCACTTAATCCACAAAACTACATTAACCGATAACA
131 CTCTAAAAATGAAGTAGCTATACAAATTCCTCACTTAATCCACAAAACTACATTAACCGATAACA
774715 ATAGCTGTAATTCAAATAAATGGG
196 ATAGCTGTAATTCAAATAAATGGG
774739 TCTCGATATT
Statistics
Matches: 217, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
219 217 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (219 bp):
GCGGGCTCACTGGTGAAAAGAGGGTTACATCAGGCTCCCTTCCTAATGAGCTTTTACCCTTTCAG
ATTAGTAAACAACGATATCAAAATAGGCAGTCCTCTTTTACTCTTATTTCACCAGAAACCAAACA
CTCTAAAAATGAAGTAGCTATACAAATTCCTCACTTAATCCACAAAACTACATTAACCGATAACA
ATAGCTGTAATTCAAATAAATGGG
Found at i:784043 original size:22 final size:22
Alignment explanation
Indices: 784018--784064 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
784008 ATTTAGATTT
* *
784018 TTTATTAATTTATAATTATACA
1 TTTAGTAATTTATAATTAAACA
784040 TTTAGTAATTTATAATTAAACA
1 TTTAGTAATTTATAATTAAACA
784062 TTT
1 TTT
784065 TATAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTAGTAATTTATAATTAAACA
Found at i:792343 original size:15 final size:16
Alignment explanation
Indices: 792305--792345 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
792295 CCAGAGCCTC
* *
792305 TGAATCATTCAGTATT
1 TGAATCATTCAGCACT
792321 TGAATCATTCAGCACT
1 TGAATCATTCAGCACT
792337 T-AATCATTC
1 TGAATCATTC
792346 TGATGTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.39
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Found at i:793016 original size:16 final size:16
Alignment explanation
Indices: 792995--793054 Score: 102
Period size: 16 Copynumber: 3.6 Consensus size: 16
792985 TCAGATTCAT
792995 ATTTCAATTCTTACAG
1 ATTTCAATTCTTACAG
793011 ATTTCAATTCTTACAG
1 ATTTCAATTCTTACAG
793027 ATTTCAATTCTTTCACAG
1 ATTTCAATTC-TT-ACAG
793045 ATTTCAATTC
1 ATTTCAATTC
793055 CCTCATAAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 26 0.62
17 2 0.05
18 14 0.33
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (16 bp):
ATTTCAATTCTTACAG
Found at i:795304 original size:26 final size:26
Alignment explanation
Indices: 795271--795347 Score: 86
Period size: 26 Copynumber: 2.9 Consensus size: 26
795261 CTTATTTTAT
795271 ATTTAATAAGATTCTTTAAATTAAAA
1 ATTTAATAAGATTCTTTAAATTAAAA
* *
795297 TTTTAATATA-ATTCTTTAATCAATAAAA
1 ATTTAATA-AGATTCTTTAA--ATTAAAA
*
795325 ATTTAATAAGAAT-TTTAAATTAA
1 ATTTAATAAGATTCTTTAAATTAA
795348 CATCGACCTC
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
25 4 0.10
26 16 0.38
27 7 0.17
28 15 0.36
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (26 bp):
ATTTAATAAGATTCTTTAAATTAAAA
Found at i:795511 original size:18 final size:19
Alignment explanation
Indices: 795476--795511 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
795466 AATGATTTAA
*
795476 TTGATTTTTTTTATAAATT
1 TTGATTTTTATTATAAATT
795495 TTGATTTTTATTA-AAAT
1 TTGATTTTTATTATAAAT
795512 AAAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.64
Consensus pattern (19 bp):
TTGATTTTTATTATAAATT
Found at i:795539 original size:13 final size:13
Alignment explanation
Indices: 795523--795563 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
795513 AAAAATTATT
795523 TAAATTTTAAATA
1 TAAATTTTAAATA
**
795536 TAAAAATT--ATA
1 TAAATTTTAAATA
795547 TAAATTTTAAATA
1 TAAATTTTAAATA
795560 TAAA
1 TAAA
795564 AATTATTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
11 9 0.41
13 13 0.59
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TAAATTTTAAATA
Found at i:795540 original size:24 final size:24
Alignment explanation
Indices: 795508--795575 Score: 120
Period size: 24 Copynumber: 2.9 Consensus size: 24
795498 ATTTTTATTA
795508 AAATA-AAAAATTATTTAAATTTT
1 AAATATAAAAATTATTTAAATTTT
*
795531 AAATATAAAAATTATATAAATTTT
1 AAATATAAAAATTATTTAAATTTT
795555 AAATATAAAAATTATTTAAAT
1 AAATATAAAAATTATTTAAAT
795576 ATTTTAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
23 5 0.12
24 37 0.88
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
AAATATAAAAATTATTTAAATTTT
Found at i:795574 original size:17 final size:17
Alignment explanation
Indices: 795502--795577 Score: 54
Period size: 16 Copynumber: 4.7 Consensus size: 17
795492 ATTTTGATTT
*
795502 TTATTAAAATA-AAAAA
1 TTATTTAAATATAAAAA
**
795518 TTATTTAAAT-TTTAAA
1 TTATTTAAATATAAAAA
** *
795534 -TATAAAAATTATATAAA
1 TTATTTAAA-TATAAAAA
795551 -T-TTTAAATATAAAAA
1 TTATTTAAATATAAAAA
795566 TTATTTAAATAT
1 TTATTTAAATAT
795578 TTTAAAAAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
15 13 0.28
16 18 0.39
17 15 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTATTTAAATATAAAAA
Found at i:795604 original size:21 final size:23
Alignment explanation
Indices: 795579--795629 Score: 81
Period size: 21 Copynumber: 2.3 Consensus size: 23
795569 TTTAAATATT
795579 TTAAAAAATAAA-TATTAAAAAA
1 TTAAAAAATAAATTATTAAAAAA
795601 -T-AAAAATAAATTATTAAAAAA
1 TTAAAAAATAAATTATTAAAAAA
795622 TTAAAAAA
1 TTAAAAAA
795630 GACAATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.35
21 11 0.42
22 1 0.04
23 5 0.19
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (23 bp):
TTAAAAAATAAATTATTAAAAAA
Found at i:795625 original size:29 final size:29
Alignment explanation
Indices: 795592--795656 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
795582 AAAAATAAAT
*
795592 ATTAAAAAATAAAAAT-AAATTATTAAAAA
1 ATTAAAAAAGAAAAATAAAATT-TTAAAAA
* *
795621 ATTAAAAAAGACAATTAAAATTTTAAAAA
1 ATTAAAAAAGAAAAATAAAATTTTAAAAA
*
795650 ATCAAAA
1 ATTAAAA
795657 TAACACAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 26 0.84
30 5 0.16
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (29 bp):
ATTAAAAAAGAAAAATAAAATTTTAAAAA
Found at i:795851 original size:4 final size:4
Alignment explanation
Indices: 795842--795871 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
795832 AAAACAATCC
795842 AATA AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AA
795872 GAAAATATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:799312 original size:20 final size:20
Alignment explanation
Indices: 799287--799324 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
799277 GAAATAGTTA
*
799287 TAAATAATTATATTTAAATT
1 TAAATAAATATATTTAAATT
799307 TAAATAAATATATTTAAA
1 TAAATAAATATATTTAAA
799325 AAATAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAATAAATATATTTAAATT
Found at i:799334 original size:13 final size:14
Alignment explanation
Indices: 799301--799334 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
799291 TAATTATATT
799301 TAAATTTAAATAAA
1 TAAATTTAAATAAA
*
799315 TATATTTAAA-AAA
1 TAAATTTAAATAAA
799328 TAAATTT
1 TAAATTT
799335 TGAATGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAATTTAAATAAA
Found at i:804218 original size:17 final size:18
Alignment explanation
Indices: 804185--804219 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
804175 CATCCATCTG
804185 GGTCTTCTGTGTAGAAAC
1 GGTCTTCTGTGTAGAAAC
*
804203 GGTCTTGTGT-TAGAAAC
1 GGTCTTCTGTGTAGAAAC
804220 TTGGCCTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.23, C:0.14, G:0.29, T:0.34
Consensus pattern (18 bp):
GGTCTTCTGTGTAGAAAC
Found at i:805635 original size:18 final size:19
Alignment explanation
Indices: 805612--805648 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
805602 CCAGTAATCC
805612 TATTCCC-TGGTAATCTTT
1 TATTCCCATGGTAATCTTT
805630 TATTCCCATTGGTAATCTT
1 TATTCCCA-TGGTAATCTT
805649 ACATTCCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.49
Consensus pattern (19 bp):
TATTCCCATGGTAATCTTT
Found at i:816751 original size:31 final size:29
Alignment explanation
Indices: 816698--816781 Score: 96
Period size: 31 Copynumber: 2.8 Consensus size: 29
816688 TTTTATGTAC
816698 TTAAAGTATTTTTTTATCAAAATAATTAT
1 TTAAAGTATTTTTTTATCAAAATAATTAT
* * *
816727 TTAAAGTTATCTTTTTAGTTAAAATATTTAT
1 TTAAAG-TATTTTTTTA-TCAAAATAATTAT
*
816758 CTAAAGTATTTTTTTTTATCAAAA
1 TTAAAGTA--TTTTTTTATCAAAA
816782 ATAGGTACAT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
29 6 0.13
30 11 0.24
31 21 0.47
32 7 0.16
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (29 bp):
TTAAAGTATTTTTTTATCAAAATAATTAT
Found at i:828423 original size:48 final size:48
Alignment explanation
Indices: 828343--828438 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 48
828333 TATCATGACC
* *
828343 ATTTAATCATGGCAATTTCAGTCTGATCTTCAATGTTTTAATTTTATA
1 ATTTAATCATGGCAATTTCAATCCGATCTTCAATGTTTTAATTTTATA
*
828391 ATTTAATCATGGCAATTTCAATCCGATTTTCAATGTTTTAATTTTATA
1 ATTTAATCATGGCAATTTCAATCCGATCTTCAATGTTTTAATTTTATA
828439 TTCAAATTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.48
Consensus pattern (48 bp):
ATTTAATCATGGCAATTTCAATCCGATCTTCAATGTTTTAATTTTATA
Found at i:828844 original size:24 final size:25
Alignment explanation
Indices: 828817--828901 Score: 88
Period size: 24 Copynumber: 3.5 Consensus size: 25
828807 AAATTGAACG
* *
828817 ACCGGTTTTTTT-ACTGGATTAAAA
1 ACCGGTTTTTTTAACCGGATAAAAA
828841 ACCGGTTTTTTTCAAACCGGATAAAAA
1 ACCGGTTTTTTT--AACCGGATAAAAA
*
828868 ACCGG-TTTTTTATCCGG--AAAAA
1 ACCGGTTTTTTTAACCGGATAAAAA
*
828890 TCCGGTTTTTTT
1 ACCGGTTTTTTT
828902 TTTAAAACCG
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
22 9 0.17
23 6 0.11
24 17 0.32
26 6 0.11
27 15 0.28
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (25 bp):
ACCGGTTTTTTTAACCGGATAAAAA
Found at i:836424 original size:15 final size:15
Alignment explanation
Indices: 836404--836437 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
836394 TGATTCCTAA
836404 GTTGTAATGTACCAT
1 GTTGTAATGTACCAT
836419 GTTGTAATGTACCAT
1 GTTGTAATGTACCAT
836434 GTTG
1 GTTG
836438 CAATAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.41
Consensus pattern (15 bp):
GTTGTAATGTACCAT
Found at i:836605 original size:24 final size:24
Alignment explanation
Indices: 836574--836621 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
836564 CTTGCAGAAA
836574 CAGCTGCTCTTTCACGAGCCTCTG
1 CAGCTGCTCTTTCACGAGCCTCTG
*
836598 CAGCTGCTCTTTCTCGAGCCTCTG
1 CAGCTGCTCTTTCACGAGCCTCTG
836622 AAGCAGCCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.10, C:0.38, G:0.21, T:0.31
Consensus pattern (24 bp):
CAGCTGCTCTTTCACGAGCCTCTG
Found at i:840238 original size:2 final size:2
Alignment explanation
Indices: 840231--840259 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
840221 TATTAAAAAT
840231 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
840260 TAATTTAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:851466 original size:62 final size:61
Alignment explanation
Indices: 851385--851516 Score: 167
Period size: 62 Copynumber: 2.1 Consensus size: 61
851375 GCTTATTTCT
*
851385 AAATAGGTACATAAAGTATACAACATTTTTCATCCAAGTACCTAAAGTATTTTTTTTGGTC
1 AAATAGGTACATAAAGTATACAACATTTTTCATCCAAGTACCTAAAGTATTTTTTTTAGTC
* * * * * * *
851446 AAAGTAGGTATC-TAAAGTATACCACCTTTTTCATCTAGGTATCTGAAGTGTTTTTTTTAGTC
1 AAA-TAGGTA-CATAAAGTATACAACATTTTTCATCCAAGTACCTAAAGTATTTTTTTTAGTC
851508 AAATAGGTA
1 AAATAGGTA
851517 GTATACCATA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
61 9 0.15
62 51 0.84
63 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (61 bp):
AAATAGGTACATAAAGTATACAACATTTTTCATCCAAGTACCTAAAGTATTTTTTTTAGTC
Found at i:851668 original size:59 final size:59
Alignment explanation
Indices: 851596--851737 Score: 149
Period size: 59 Copynumber: 2.4 Consensus size: 59
851586 TAACTAAGTA
* * * * * *
851596 AAAAAGTGTTATACTTTAGGTACCTACTTTGACCAAAAAACACTTTTGATACCTATATG
1 AAAAAGTGGTATACTTTAAGTACCTACTTCGACAAAAAAACACTTTAGATACCTAGATG
* ** * * * * *
851655 AAAAAGTGGTATACGTTAAGCGCTTACTTCGATAAAAAAATACTTTAGGTACTTAGATG
1 AAAAAGTGGTATACTTTAAGTACCTACTTCGACAAAAAAACACTTTAGATACCTAGATG
851714 AAAAAGATGGTATACTTTAAGTAC
1 AAAAAG-TGGTATACTTTAAGTAC
851738 TTATTTTTTA
Statistics
Matches: 65, Mismatches: 17, Indels: 1
0.78 0.20 0.01
Matches are distributed among these distances:
59 51 0.78
60 14 0.22
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.32
Consensus pattern (59 bp):
AAAAAGTGGTATACTTTAAGTACCTACTTCGACAAAAAAACACTTTAGATACCTAGATG
Found at i:854895 original size:42 final size:40
Alignment explanation
Indices: 854846--854937 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 40
854836 ATTTTGTAAC
* * **
854846 AATATATTTATAATTATTTATTATATTTTAAATTGTTAAAA
1 AATATATTTATAATAACTT-TTATATTTTAAATAATTAAAA
*
854887 TAATATATTTTATAATAACTTTTATATTTTTAATAATTAAAA
1 -AATATA-TTTATAATAACTTTTATATTTTAAATAATTAAAA
854929 AATATATTT
1 AATATATTT
854938 TAACAATATA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
40 3 0.07
41 6 0.14
42 24 0.55
43 11 0.25
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (40 bp):
AATATATTTATAATAACTTTTATATTTTAAATAATTAAAA
Found at i:855247 original size:14 final size:14
Alignment explanation
Indices: 855228--855256 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
855218 ATCATGCGAG
855228 AAGCAATATCCTAA
1 AAGCAATATCCTAA
855242 AAGCAATATCCTAA
1 AAGCAATATCCTAA
855256 A
1 A
855257 TTTGACGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.21, G:0.07, T:0.21
Consensus pattern (14 bp):
AAGCAATATCCTAA
Found at i:857161 original size:20 final size:19
Alignment explanation
Indices: 857115--857162 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
857105 ATGACCAACA
* * *
857115 AAATCGTAATGCGATCTCT
1 AAATCGCAACGCGATCTCC
857134 AAATCGCAACGCGATCTCC
1 AAATCGCAACGCGATCTCC
857153 AATATCGCAA
1 AA-ATCGCAA
857163 ATCATTTTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCC
Found at i:857199 original size:40 final size:41
Alignment explanation
Indices: 857137--857221 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 41
857127 GATCTCTAAA
857137 TCGCAACGCGATCTCCAATATCGCAAAT-C-ATTTTCCAAAT
1 TCGCAACGCGATCTCCAATATCGC-AATGCGATTTTCCAAAT
* ** * *
857177 TCGCAACGCGATTTTGACTATCGCATTGCGATTTTCCAAAT
1 TCGCAACGCGATCTCCAATATCGCAATGCGATTTTCCAAAT
857218 TCGC
1 TCGC
857222 GTTGCGATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
39 2 0.05
40 21 0.55
41 15 0.39
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (41 bp):
TCGCAACGCGATCTCCAATATCGCAATGCGATTTTCCAAAT
Found at i:857226 original size:21 final size:21
Alignment explanation
Indices: 857196--857249 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
857186 GATTTTGACT
857196 ATCGCATTGCGATTTTCCAAA
1 ATCGCATTGCGATTTTCCAAA
* *
857217 TTCGCGTTGCGATTTTCCAAA
1 ATCGCATTGCGATTTTCCAAA
857238 ATCGCATTGCGA
1 ATCGCATTGCGA
857250 ATATGTAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (21 bp):
ATCGCATTGCGATTTTCCAAA
Found at i:857281 original size:20 final size:20
Alignment explanation
Indices: 857258--857304 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
857248 GAATATGTAA
*
857258 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCAATTCTGACT
*
857278 ATCGCAACGCAATTGTGACT
1 ATCGCAACGCAATTCTGACT
857298 ATCGCAA
1 ATCGCAA
857305 TACTGAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCAATTCTGACT
Found at i:857494 original size:17 final size:17
Alignment explanation
Indices: 857472--857506 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
857462 CGACATCCGT
*
857472 TCCTATATCTAACGACA
1 TCCTATATCCAACGACA
857489 TCCTATATCCAACGACA
1 TCCTATATCCAACGACA
857506 T
1 T
857507 TCTTCCCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.31, G:0.06, T:0.29
Consensus pattern (17 bp):
TCCTATATCCAACGACA
Found at i:858189 original size:24 final size:24
Alignment explanation
Indices: 858162--858215 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
858152 GTATTCGAAA
858162 TTTGATATTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* * *
858186 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
858210 TTTGAT
1 TTTGAT
858216 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:860491 original size:12 final size:12
Alignment explanation
Indices: 860474--860508 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
860464 CAAACGAAAG
860474 GCAATCAAAATT
1 GCAATCAAAATT
860486 GCAATCAAAATT
1 GCAATCAAAATT
*
860498 ACAATCAAAAT
1 GCAATCAAAAT
860509 CAAAATCCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.54, C:0.17, G:0.06, T:0.23
Consensus pattern (12 bp):
GCAATCAAAATT
Found at i:860520 original size:18 final size:18
Alignment explanation
Indices: 860488--860522 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
860478 TCAAAATTGC
*
860488 AATCAAAATTACAATCAA
1 AATCAAAATCACAATCAA
*
860506 AATCAAAATCCCAATCA
1 AATCAAAATCACAATCA
860523 CAACCGGCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (18 bp):
AATCAAAATCACAATCAA
Found at i:860718 original size:20 final size:20
Alignment explanation
Indices: 860693--860877 Score: 196
Period size: 20 Copynumber: 9.8 Consensus size: 20
860683 TTACACATTC
* *
860693 ATTTGAATATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
*
860713 ATTTGACTATCGCAAAGCGA
1 ATTTGACTATCGCAACGCGA
860733 ATTTGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
* *
860752 A----A-AATCGCAACTCGA
1 ATTTGACTATCGCAACGCGA
860767 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
860787 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
*
860807 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
860827 A----A--ATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
860841 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
860861 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
860878 TGAAATCAAC
Statistics
Matches: 137, Mismatches: 16, Indels: 24
0.77 0.09 0.14
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 1 0.01
18 1 0.01
19 3 0.02
20 110 0.80
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:860768 original size:34 final size:34
Alignment explanation
Indices: 860721--860858 Score: 152
Period size: 34 Copynumber: 3.9 Consensus size: 34
860711 GAATTTGACT
860721 ATCGCAAAGCGAATTTGACTATCGCAACGCAAAA
1 ATCGCAAAGCGAATTTGACTATCGCAACGCAAAA
** *
860755 ATCGCAACTCGAATTTGACTATCGCAACGCGAATTTGATT
1 ATCGCAAAGCGAATTTGACTATCGCAACGC-AA----A-A
* *
860795 ATCGCAACGGGAATTTGACTATCGCAACG-AGAAA
1 ATCGCAAAGCGAATTTGACTATCGCAACGCA-AAA
*
860829 ATCGCAAAGCGTATTTGACTATCGCAACGC
1 ATCGCAAAGCGAATTTGACTATCGCAACGC
860859 GAATTTGACT
Statistics
Matches: 87, Mismatches: 9, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
34 54 0.62
35 3 0.03
38 1 0.01
39 2 0.02
40 27 0.31
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (34 bp):
ATCGCAAAGCGAATTTGACTATCGCAACGCAAAA
Found at i:860787 original size:54 final size:54
Alignment explanation
Indices: 860701--860803 Score: 172
Period size: 54 Copynumber: 1.9 Consensus size: 54
860691 TCATTTGAAT
860701 ATCGCAATGCGAATTTGACTATCGCAAAGCGAATTTGACTATCGCAACGCAAAA
1 ATCGCAATGCGAATTTGACTATCGCAAAGCGAATTTGACTATCGCAACGCAAAA
* *
860755 ATCGCAACT-CGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACG
1 ATCGCAA-TGCGAATTTGACTATCGCAAAGCGAATTTGACTATCGCAACG
860804 GGAATTTGAC
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
54 45 0.98
55 1 0.02
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (54 bp):
ATCGCAATGCGAATTTGACTATCGCAAAGCGAATTTGACTATCGCAACGCAAAA
Found at i:860814 original size:74 final size:74
Alignment explanation
Indices: 860693--860877 Score: 282
Period size: 74 Copynumber: 2.5 Consensus size: 74
860683 TTACACATTC
* * *
860693 ATTTGAATATCGCAATGCGAATTTGACTATCGCAAAGCGAATTTGACTATCGCAACGCA-AAAAT
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACG-AGAAAAT
**
860757 CGCAACTCGA
65 CGCAAAGCGA
* *
860767 ATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGGAATTTGACTATCGCAACGAGAAAATC
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAGAAAATC
*
860832 GCAAAGCGT
66 GCAAAGCGA
860841 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACG
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACG
860878 TGAAATCAAC
Statistics
Matches: 101, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
73 1 0.01
74 100 0.99
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (74 bp):
ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAGAAAATC
GCAAAGCGA
Found at i:860833 original size:54 final size:54
Alignment explanation
Indices: 860775--860882 Score: 171
Period size: 54 Copynumber: 2.0 Consensus size: 54
860765 GAATTTGACT
* * *
860775 ATCGCAACGCGAATTTGATTATCGCAACGGGAATTTGACTATCGCAACGAGAAA
1 ATCGCAAAGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAGAAA
* *
860829 ATCGCAAAGCGTATTTGACTATCGCAACGCGAATTTGACTATCGCAACGTGAAA
1 ATCGCAAAGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAGAAA
860883 TCAACAAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.23
Consensus pattern (54 bp):
ATCGCAAAGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAGAAA
Found at i:861022 original size:67 final size:65
Alignment explanation
Indices: 860910--861081 Score: 163
Period size: 73 Copynumber: 2.5 Consensus size: 65
860900 TATTGAAATC
*
860910 AACAAATCAACTTTTACATTTCAATCAATTAAACAAGCACAAATAAGAA-TTATTTAT-ACATCA
1 AACAAATCAACTTTTACA--T-AATCAATTAAACAAGCAAAAATAAGAATTTATTT-TCACATCA
860973 ATTA
62 ATTA
* *
860977 AACAAATCAACTTTTACA-AATCAATTAAACAAGCAAAAAATAATAATAATTCTTATTTTCCTCA
1 AACAAATCAACTTTTACATAATCAATTAAACAAGC---AAA-AATAAGAA-T-TTATTTT-CACA
861041 TCAATTA
59 TCAATTA
*
861048 AACAAAAATCAACTTTTA-AGAATCAATTAAACAA
1 AAC--AAATCAACTTTTACATAATCAATTAAACAA
861082 TAAAAAAAAG
Statistics
Matches: 90, Mismatches: 3, Indels: 18
0.81 0.03 0.16
Matches are distributed among these distances:
63 16 0.18
66 2 0.02
67 25 0.28
69 1 0.01
70 6 0.07
71 12 0.13
72 1 0.01
73 27 0.30
ACGTcount: A:0.51, C:0.16, G:0.02, T:0.30
Consensus pattern (65 bp):
AACAAATCAACTTTTACATAATCAATTAAACAAGCAAAAATAAGAATTTATTTTCACATCAATTA
Found at i:861593 original size:15 final size:15
Alignment explanation
Indices: 861568--861639 Score: 101
Period size: 15 Copynumber: 4.9 Consensus size: 15
861558 TGGTTTTCCA
861568 GAAAATGAATTACTG
1 GAAAATGAATTACTG
**
861583 GAATTTGAATTACTG
1 GAAAATGAATTACTG
861598 GAAAATGAATTACTG
1 GAAAATGAATTACTG
**
861613 GAATTTGAATT-CTG
1 GAAAATGAATTACTG
861627 GAAAATGAATTAC
1 GAAAATGAATTAC
861640 ATTTCTGTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
14 12 0.25
15 36 0.75
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (15 bp):
GAAAATGAATTACTG
Found at i:861637 original size:29 final size:30
Alignment explanation
Indices: 861568--861639 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
861558 TGGTTTTCCA
861568 GAAAATGAATTACTGGAATTTGAATTACTG
1 GAAAATGAATTACTGGAATTTGAATTACTG
861598 GAAAATGAATTACTGGAATTTGAATT-CTG
1 GAAAATGAATTACTGGAATTTGAATTACTG
861627 GAAAATGAATTAC
1 GAAAATGAATTAC
861640 ATTTCTGTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 16 0.38
30 26 0.62
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (30 bp):
GAAAATGAATTACTGGAATTTGAATTACTG
Found at i:861645 original size:20 final size:20
Alignment explanation
Indices: 861622--861691 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
861612 GGAATTTGAA
861622 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
861642 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
861662 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
861682 TTCTGGAAAA
1 TTCTGGAAAA
861692 CATCTGGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:861899 original size:28 final size:27
Alignment explanation
Indices: 861858--861922 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 27
861848 TTTACTAAAA
*
861858 TATTATTGAAATATATAAATAATATTAT
1 TATTATT-AAATATATAAAAAATATTAT
*
861886 TCATTATTAAATATATAAAAAATTTTAT
1 T-ATTATTAAATATATAAAAAATATTAT
861914 TATATATTA
1 TAT-TATTA
861923 TTATAATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 25 0.76
29 6 0.18
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
TATTATTAAATATATAAAAAATATTAT
Found at i:861949 original size:49 final size:51
Alignment explanation
Indices: 861876--861980 Score: 117
Period size: 52 Copynumber: 2.1 Consensus size: 51
861866 AAATATATAA
* * *
861876 ATAATATTATTCATTATTAAATAT-ATA-AAAAATTTTAT-TATATATTATT
1 ATAATATAATTCATTATTAAATATAATATAAAAATATAATAT-TATATTATT
* **
861925 ATAATATAATTGATTATTTTATATAATATTAAAAATATAATATTATATTATT
1 ATAATATAATTCATTATTAAATATAATA-TAAAAATATAATATTATATTATT
861977 ATAA
1 ATAA
861981 ATATTAATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
49 20 0.43
50 3 0.07
52 22 0.48
53 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (51 bp):
ATAATATAATTCATTATTAAATATAATATAAAAATATAATATTATATTATT
Found at i:861971 original size:22 final size:23
Alignment explanation
Indices: 861946--861989 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
861936 GATTATTTTA
861946 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
861968 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
861990 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:861990 original size:26 final size:24
Alignment explanation
Indices: 861961--862023 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
861951 TATTAAAAAT
861961 ATAATATTATATTATTATAA-ATATTA
1 ATAATA-TATATT-TTA-AATATATTA
*
861987 ATAA-ATATATTTTAAATATTTTA
1 ATAATATATATTTTAAATATATTA
862010 ATAAT-TAATATTTT
1 ATAATAT-ATATTTT
862024 GATGAAAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 13 0.39
24 13 0.39
25 1 0.03
26 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATAATATATATTTTAAATATATTA
Found at i:861994 original size:22 final size:22
Alignment explanation
Indices: 861950--862006 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
861940 ATTTTATATA
* *
861950 ATATTAAAAATA-TAATATTAT
1 ATATTATAAATATTAATATAAT
861971 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
861993 ATATTTTAAATATT
1 ATATTATAAATATT
862007 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:862254 original size:42 final size:42
Alignment explanation
Indices: 862195--862314 Score: 231
Period size: 42 Copynumber: 2.9 Consensus size: 42
862185 ATGAATTACA
*
862195 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
862237 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
862279 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
862315 TTCGGGGAAA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:863277 original size:42 final size:42
Alignment explanation
Indices: 863218--863340 Score: 133
Period size: 42 Copynumber: 2.9 Consensus size: 42
863208 GTGAATCGGG
* *
863218 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGGAGC
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGAGC
** * *
863260 CTCTTGAACGGTGGGAGGGGA-CTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACCTCTTGAACGATGACAGGAGC
* * *
863302 CTCTTGAACGATAGGAGAGG-CCTTTTGAACGATGACAGG
1 CTCTTGAACGGTGGGAG-GGACCTCTTGAACGATGACAGG
863341 TGAGTCGGGC
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
41 1 0.02
42 61 0.92
43 4 0.06
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGAGC
Found at i:863284 original size:21 final size:21
Alignment explanation
Indices: 863218--863287 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
863208 GTGAATCGGG
*
863218 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
863238 CCTCTTCAACGATGACAGGAGC
1 -CTCTTGAACGGTGGGAGGGGA
863260 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
863281 CTCTTGA
1 CTCTTGA
863288 GGGATGATAG
Statistics
Matches: 35, Mismatches: 13, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
21 33 0.94
22 2 0.06
ACGTcount: A:0.21, C:0.20, G:0.36, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:872481 original size:20 final size:22
Alignment explanation
Indices: 872450--872503 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 22
872440 TCATATTATT
*
872450 TTATTT-TTTTTCTT-TTAA-A
1 TTATTTATTTTTCTTATAAATA
872469 TTATTTATTTTTCTTATAAATA
1 TTATTTATTTTTCTTATAAATA
872491 TTATATTATTTTT
1 TTAT-TTATTTTT
872504 ATATAATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 6 0.20
20 8 0.27
21 3 0.10
22 5 0.17
23 8 0.27
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (22 bp):
TTATTTATTTTTCTTATAAATA
Found at i:872505 original size:20 final size:19
Alignment explanation
Indices: 872451--872511 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 19
872441 CATATTATTT
*
872451 TATTT-TTTTTCTTTTAAA
1 TATTTATTTTTCTTATAAA
872469 TTATTTATTTTTCTTATAAA
1 -TATTTATTTTTCTTATAAA
872489 TATTATATTATTT-TTATATAA
1 TATT-TATT-TTTCTTATA-AA
872510 TA
1 TA
872512 ATGATTTAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
19 9 0.24
20 21 0.57
21 7 0.19
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (19 bp):
TATTTATTTTTCTTATAAA
Found at i:872508 original size:22 final size:22
Alignment explanation
Indices: 872468--872509 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
872458 TTTCTTTTAA
*
872468 ATTATTTATTTTTCTTATAAAT
1 ATTATTTATTTTTCATATAAAT
872490 ATTATATTATTTTT-ATATAA
1 ATTAT-TTATTTTTCATATAA
872510 TAATGATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTATTTATTTTTCATATAAAT
Found at i:874384 original size:20 final size:20
Alignment explanation
Indices: 874359--874603 Score: 267
Period size: 20 Copynumber: 12.2 Consensus size: 20
874349 TGCCCTACCG
* *
874359 GATTTACAGATTCTCGTTGC
1 GATTTACGGATTCGCGTTGC
**
874379 GATTTACGGATTATCGTTGC
1 GATTTACGGATTCGCGTTGC
**
874399 GATTTACGGATTATCGTTGC
1 GATTTACGGATTCGCGTTGC
*
874419 GATTTACGGATTCTCGTTGC
1 GATTTACGGATTCGCGTTGC
**
874439 GATTTACGGATTATCGTTGC
1 GATTTACGGATTCGCGTTGC
*
874459 GATTTACGGATACGCGTTGC
1 GATTTACGGATTCGCGTTGC
* * *
874479 GATATACGGATACGCATTGC
1 GATTTACGGATTCGCGTTGC
** *
874499 GATTTACCCATACGCGTTGC
1 GATTTACGGATTCGCGTTGC
* *
874519 GATTTACGGATACACGTTGC
1 GATTTACGGATTCGCGTTGC
*
874539 GATTTACGGATACGCGTTGC
1 GATTTACGGATTCGCGTTGC
*
874559 GATTTATGTG-TTCGCGTTGC
1 GATTTACG-GATTCGCGTTGC
* **
874579 GATTTTCATATTCGCGTTGC
1 GATTTACGGATTCGCGTTGC
874599 GATTT
1 GATTT
874604 TGGAAAATCG
Statistics
Matches: 200, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
20 199 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GATTTACGGATTCGCGTTGC
Found at i:874620 original size:21 final size:21
Alignment explanation
Indices: 874590--874672 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
874580 ATTTTCATAT
*
874590 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
874611 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
874632 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
874653 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
874673 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:874663 original size:42 final size:43
Alignment explanation
Indices: 874570--874668 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
874560 ATTTATGTGT
* *
874570 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
874611 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
874653 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
874669 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:875003 original size:21 final size:20
Alignment explanation
Indices: 874918--875074 Score: 84
Period size: 21 Copynumber: 7.8 Consensus size: 20
874908 AATGACCAAT
** *
874918 AAAATCGCAACGCGA-AATA
1 AAAATCGCAACGCGATTTTC
***
874937 AAAATCGCAACGCGATCCCC
1 AAAATCGCAACGCGATTTTC
* ** *
874957 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGA-TTTTC
*
874977 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTC
* * *
874998 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGAT-TTTC
* **
875019 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTT-C
* * *
875040 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTC
875060 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
875075 ACACATAAAT
Statistics
Matches: 104, Mismatches: 28, Indels: 11
0.73 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTC
Found at i:875103 original size:20 final size:20
Alignment explanation
Indices: 875041--875233 Score: 228
Period size: 20 Copynumber: 9.7 Consensus size: 20
875031 CGATTTTCCA
* ** *
875041 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
875061 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
875081 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
875101 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
875121 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
875141 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
875161 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
875181 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* *
875201 AAATCGCAACGAGAATCCGT
1 AAATCGCAACGCGTATCCGT
875221 AAATCGCAACGCG
1 AAATCGCAACGCG
875234 ATATTTAAAG
Statistics
Matches: 148, Mismatches: 21, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
19 2 0.01
20 144 0.97
21 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:875778 original size:21 final size:20
Alignment explanation
Indices: 875734--875791 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
875724 TGCAGAAGAG
***
875734 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
875754 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
*
875775 TCGCAACGCGA-AATGAA
1 TCGCAACGAGAGAATGAA
875792 GTCAGCCTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 6 0.18
20 12 0.36
21 15 0.45
ACGTcount: A:0.43, C:0.19, G:0.26, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:876727 original size:14 final size:14
Alignment explanation
Indices: 876708--876743 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
876698 ATTGTTTAAT
876708 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
876722 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
876736 TGATTTGT
1 TGATTTGT
876744 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:876862 original size:19 final size:19
Alignment explanation
Indices: 876846--876943 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
876836 AAAAATGACT
876846 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
876865 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
876884 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
876898 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
876917 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
876937 ATCGCAA
1 ATCGCAA
876944 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:876975 original size:53 final size:53
Alignment explanation
Indices: 876846--876962 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
876836 AAAAATGACT
876846 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
876898 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
876951 ATCGCAATGCGA
1 ATCGCAATGCGA
876963 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:876980 original size:19 final size:19
Alignment explanation
Indices: 876952--877173 Score: 232
Period size: 19 Copynumber: 12.7 Consensus size: 19
876942 AACGAGAGAA
*
876952 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
876971 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
876990 TCGCATTGCGA--TT-ATC
1 TCGCATTGCGATTTTCATT
877006 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
877023 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
877042 TCACATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
877058 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
877075 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
877094 TCGCATTGCGGTTTTC---
1 TCGCATTGCGATTTTCATT
*
877110 TCG--TTGCGATTTTTATTT
1 TCGCATTGCGATTTTCA-TT
877128 TCGCATTGCGATTTTCA--
1 TCGCATTGCGATTTTCATT
*
877145 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
877161 TCGCATTGCGATT
1 TCGCATTGCGATT
877174 CTCTCGTTGC
Statistics
Matches: 169, Mismatches: 13, Indels: 42
0.75 0.06 0.19
Matches are distributed among these distances:
14 32 0.19
16 18 0.11
17 16 0.09
18 3 0.02
19 89 0.53
20 11 0.07
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:877015 original size:52 final size:52
Alignment explanation
Indices: 876958--877145 Score: 322
Period size: 52 Copynumber: 3.6 Consensus size: 52
876948 AGAATCGCAA
876958 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGT
* *
877010 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCACATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGT
* *
877062 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGGTTTTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGT
*
877114 TGCGATTTTTATTTTCGCATTGCGATTTTCAT
1 TGCGATTTTCA-TTTCGCATTGCGATTTTCAT
877146 GTTGGGATTT
Statistics
Matches: 129, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
52 109 0.84
53 20 0.16
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.48
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTATCTCGT
Found at i:877195 original size:33 final size:33
Alignment explanation
Indices: 876976--877187 Score: 189
Period size: 33 Copynumber: 6.2 Consensus size: 33
876966 TCATTTCGCA
*
876976 TTGCGATTTTCATTTCGCATTGCGATTATCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* *
877009 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCACA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC---TCTCG
* * * * *
877047 TTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
* *
877080 TTGCGATTTTCATTTCGCATTGCGGTTTTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* *
877113 TTGCGATTTTTATTTTCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCA-TTTCGCATTGCGATTCTC-TCG
*
877147 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
877180 TTGCGATT
1 TTGCGATT
877188 GTAATTTCCG
Statistics
Matches: 146, Mismatches: 19, Indels: 28
0.76 0.10 0.15
Matches are distributed among these distances:
31 9 0.06
32 5 0.03
33 76 0.52
34 28 0.19
35 3 0.02
37 2 0.01
38 11 0.08
39 3 0.02
40 9 0.06
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:877903 original size:34 final size:32
Alignment explanation
Indices: 877850--877919 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
877840 ACCTTACAAC
*
877850 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
877882 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
877916 TCCC
1 TCCC
877920 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:878228 original size:21 final size:21
Alignment explanation
Indices: 878202--878243 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
878192 CCAGAATGGG
878202 GGGAATCGGTACCCCTTCATA
1 GGGAATCGGTACCCCTTCATA
878223 GGGAATCGGTACCCCTTCATA
1 GGGAATCGGTACCCCTTCATA
878244 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (21 bp):
GGGAATCGGTACCCCTTCATA
Found at i:878322 original size:22 final size:21
Alignment explanation
Indices: 878279--878318 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
878269 CTGTTGAACA
878279 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
878300 GGGGGGAATCGGTACCCCC
1 GGGGGGAATCGGTACCCCC
878319 CTGGACATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.30, G:0.42, T:0.12
Consensus pattern (21 bp):
GGGGGGAATCGGTACCCCCTG
Found at i:878380 original size:21 final size:21
Alignment explanation
Indices: 878355--878433 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
878345 AAAACCTGCA
878355 GGGGGAATCTGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
*
878376 GGGGGTATCTGTA--CCC---
1 GGGGGAATCTGTACCCCCTGG
*
878392 -GGGGTATCTGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
*
878412 GGGGGAATCTATACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
878433 G
1 G
878434 CAATCTTGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
19 3 0.06
21 31 0.63
ACGTcount: A:0.14, C:0.28, G:0.37, T:0.22
Consensus pattern (21 bp):
GGGGGAATCTGTACCCCCTGG
Found at i:878397 original size:15 final size:15
Alignment explanation
Indices: 878377--878406 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
878367 ACCCCCTGGG
878377 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
878392 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
878407 CCTGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:878408 original size:36 final size:36
Alignment explanation
Indices: 878356--878427 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
878346 AAACCTGCAG
* *
878356 GGGGAATCTGTACCCCCTGGGGGGGTATCTGTACCC
1 GGGGAATCTGTACCCCCTGGGGGGGAATCTATACCC
*
878392 GGGGTATCTGTACCCCCTGGGGGGGAATCTATACCC
1 GGGGAATCTGTACCCCCTGGGGGGGAATCTATACCC
878428 CCTGGGCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.15, C:0.28, G:0.35, T:0.22
Consensus pattern (36 bp):
GGGGAATCTGTACCCCCTGGGGGGGAATCTATACCC
Found at i:878555 original size:29 final size:31
Alignment explanation
Indices: 878523--878582 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
878513 AAACTTTGAA
878523 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
878552 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
878583 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:878772 original size:22 final size:22
Alignment explanation
Indices: 878741--878810 Score: 122
Period size: 22 Copynumber: 3.1 Consensus size: 22
878731 AAGCTCCCCC
*
878741 TTTTTCATTAAGAAATTGAATT
1 TTTTTTATTAAGAAATTGAATT
878763 TTTTTTATTAAGAAATTGAATTT
1 TTTTTTATTAAGAAATTGAA-TT
878786 TTTTTTATTAAGAAATTGAATT
1 TTTTTTATTAAGAAATTGAATT
878808 TTT
1 TTT
878811 CAAACCAAAC
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
22 24 0.52
23 22 0.48
ACGTcount: A:0.34, C:0.01, G:0.09, T:0.56
Consensus pattern (22 bp):
TTTTTTATTAAGAAATTGAATT
Found at i:880780 original size:12 final size:12
Alignment explanation
Indices: 880763--880787 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
880753 TCTTCGGGGA
880763 CTTTTTCTTCTT
1 CTTTTTCTTCTT
880775 CTTTTTCTTCTT
1 CTTTTTCTTCTT
880787 C
1 C
880788 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:881745 original size:20 final size:20
Alignment explanation
Indices: 881720--882004 Score: 329
Period size: 20 Copynumber: 14.2 Consensus size: 20
881710 TGCCCTACCG
*
881720 GATTTACAGATTCTCGTTGC
1 GATTTACGGATTCTCGTTGC
*
881740 GATTTACGGATTATCGTTGC
1 GATTTACGGATTCTCGTTGC
*
881760 GATTTACGGATTATCGTTGC
1 GATTTACGGATTCTCGTTGC
*
881780 GATTTACGGATTATCGTTGC
1 GATTTACGGATTCTCGTTGC
881800 GATTTACGGATTCTCGTTGC
1 GATTTACGGATTCTCGTTGC
881820 GATTTACGGATTCTCGTTGC
1 GATTTACGGATTCTCGTTGC
*
881840 GATTTACGGATTATCGTTGC
1 GATTTACGGATTCTCGTTGC
* *
881860 GATTTACGGATACGCGTTGC
1 GATTTACGGATTCTCGTTGC
* * * *
881880 GATATACGGATACGCATTGC
1 GATTTACGGATTCTCGTTGC
** * *
881900 GATTTACCCATACGCGTTGC
1 GATTTACGGATTCTCGTTGC
* *
881920 GATTTACGGATACACGTTGC
1 GATTTACGGATTCTCGTTGC
* *
881940 GATTTACGGATACGCGTTGC
1 GATTTACGGATTCTCGTTGC
* *
881960 GATTTATGTG-TTCGCGTTGC
1 GATTTACG-GATTCTCGTTGC
* ** *
881980 GATTTTCATATTCGCGTTGC
1 GATTTACGGATTCTCGTTGC
882000 GATTT
1 GATTT
882005 TGGAAAATCG
Statistics
Matches: 240, Mismatches: 23, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
20 239 1.00
21 1 0.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GATTTACGGATTCTCGTTGC
Found at i:882021 original size:21 final size:21
Alignment explanation
Indices: 881991--882073 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
881981 ATTTTCATAT
*
881991 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
882012 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
882033 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
882054 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
882074 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:882064 original size:42 final size:43
Alignment explanation
Indices: 881971--882069 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
881961 ATTTATGTGT
* *
881971 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
882012 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
882054 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
882070 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:886927 original size:19 final size:20
Alignment explanation
Indices: 886905--886943 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
886895 AATAAAAAGT
886905 TTAAAT-AAAAAATTAAAAA
1 TTAAATCAAAAAATTAAAAA
**
886924 TTAAATCAAATTATTAAAAA
1 TTAAATCAAAAAATTAAAAA
886944 AAAATTAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (20 bp):
TTAAATCAAAAAATTAAAAA
Found at i:886947 original size:32 final size:32
Alignment explanation
Indices: 886905--886965 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
886895 AATAAAAAGT
886905 TTAAATAAAAAATTAA-AAATTAAATCAAATTA
1 TTAAA-AAAAAATTAAGAAATTAAATCAAATTA
*
886937 TTAAAAAAAAATTAAGAAATTCAATCAAA
1 TTAAAAAAAAATTAAGAAATTAAATCAAA
886966 CCATTTTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 10 0.37
32 17 0.63
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.28
Consensus pattern (32 bp):
TTAAAAAAAAATTAAGAAATTAAATCAAATTA
Found at i:888085 original size:22 final size:25
Alignment explanation
Indices: 888028--888079 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
888018 TCTTAATTTA
888028 TTATGAG-AAAAAATAATCTCTAAC
1 TTATGAGAAAAAAATAATCTCTAAC
*
888052 TTATGAGAAAAAAATAATCTTTAAC
1 TTATGAGAAAAAAATAATCTCTAAC
888077 TTA
1 TTA
888080 GAAAAACACT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.33
Consensus pattern (25 bp):
TTATGAGAAAAAAATAATCTCTAAC
Found at i:898146 original size:45 final size:46
Alignment explanation
Indices: 898082--898171 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 46
898072 ATTGAGGTGT
898082 TATTATCTGATAAGATGAAGAATGATTGTTTGATTGT-AAAGTAAC
1 TATTATCTGATAAGATGAAGAATGATTGTTTGATTGTAAAAGTAAC
898127 TATTATCTGATAAGATGAAGAATGATTGTTTGATTGTAAAAGTAA
1 TATTATCTGATAAGATGAAGAATGATTGTTTGATTGTAAAAGTAA
898172 GGGGATCTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 37 0.84
46 7 0.16
ACGTcount: A:0.39, C:0.03, G:0.20, T:0.38
Consensus pattern (46 bp):
TATTATCTGATAAGATGAAGAATGATTGTTTGATTGTAAAAGTAAC
Found at i:904132 original size:35 final size:37
Alignment explanation
Indices: 904061--904133 Score: 98
Period size: 35 Copynumber: 2.0 Consensus size: 37
904051 CTTGGAAAAT
*
904061 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
*
904098 ATTTATATATTTT-TTT-ACAAAATTGAAAAT-ATAAA
1 ATTTATATATTTTCTTTAAAAAAATT-AAAATCATAAA
904133 A
1 A
904134 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 13 0.39
36 7 0.21
37 13 0.39
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
Found at i:910032 original size:10 final size:10
Alignment explanation
Indices: 910017--910049 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
910007 GAATTTGTTT
910017 AAAGTTTTCA
1 AAAGTTTTCA
910027 AAAGTTTTCA
1 AAAGTTTTCA
910037 AAAGTTTTCA
1 AAAGTTTTCA
910047 AAA
1 AAA
910050 ATAATTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (10 bp):
AAAGTTTTCA
Found at i:910361 original size:21 final size:22
Alignment explanation
Indices: 910330--910370 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
910320 TTTAAAAATA
**
910330 TAAAGGAAGTATTGATACTCAT
1 TAAAGGAAGTACCGATACTCAT
910352 TAAAGG-AGTACCGATACTC
1 TAAAGGAAGTACCGATACTC
910371 CCTGTCCTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (22 bp):
TAAAGGAAGTACCGATACTCAT
Found at i:916452 original size:112 final size:111
Alignment explanation
Indices: 916250--916824 Score: 841
Period size: 112 Copynumber: 5.1 Consensus size: 111
916240 TTATCGGTTT
** * * *
916250 GTGTCGATACTTTATAAAAAATATATTTATTCATAACAATATAATATGG--AAAAAATGATAAAA
1 GTGTCGATACTTTAT--AAAATATATCGATCCATAACAATATAACA-GGTAAAAAAATGACAAAA
* *
916313 CCGGTCTATAAATGACAAAACATGTAAAGCGCTACCGGATATATTGAAA
63 CCGGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
* *
916362 ATATCGATACTTTAATAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTT-ATAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
916427 GGTCTATAAATGACAAAACAAGTAAAGCGCTACCAAATATATTGAAA
65 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
916474 GTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTAT-AAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * *
916539 GGTTTATAAATGACAAAACAGGTAAAGCGTTACCGGATATATTGAAA
65 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
*
916586 GTGTCGATACTTTATAAAAAAAGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAAC
1 GTGTCGATACTTTAT-AAAATA-TATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAAC
*
916651 CGGTCTATAAATGACAAAACATGTAAAGCGCTACCAGATATATTGAAA
64 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
* *
916699 GTGTCGATACTTTATAGAAATGTATCGATTCATAACAATATAACAGGT-AAAAAATGACAAAACC
1 GTGTCGATACTTTATA-AAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * * *
916763 GATTTATAAATGACAAAACAGGTAAAGCGCTATCAGATATGTTGAAA
65 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
**
916810 GTGTTAATACTTTAT
1 GTGTCGATACTTTAT
916825 TATAAGTATC
Statistics
Matches: 425, Mismatches: 32, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
110 2 0.00
111 98 0.23
112 219 0.52
113 106 0.25
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.26
Consensus pattern (111 bp):
GTGTCGATACTTTATAAAATATATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCG
GTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
Found at i:917079 original size:168 final size:168
Alignment explanation
Indices: 916798--917130 Score: 567
Period size: 168 Copynumber: 2.0 Consensus size: 168
916788 AGCGCTATCA
* * *
916798 GATATGTTGAAAGTGTTAATACTTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAA
1 GATATGTTGAAAGTGTCAATACTTTATTATAAGTATCGACACTTTTAGAATTTAAAAGAAAAGAA
*
916863 GTTATAGCACTAATAAAGTGTCGATACTTTATAAAAATGTAGCGATCCATAACAATATAACAAGT
66 GTTATAGCACCAATAAAGTGTCGATACTTTATAAAAATGTAGCGATCCATAACAATATAACAAGT
* *
916928 AAAAATATGATAAAATCGATCTCGAAATGACAAAACCG
131 AAAAAAATGACAAAATCGATCTCGAAATGACAAAACCG
*
916966 GATATGTTGAAAGTGTCGATACTTTATTATAAGTATCGACACTTTTAGAATTTAAAAGAAAAGAA
1 GATATGTTGAAAGTGTCAATACTTTATTATAAGTATCGACACTTTTAGAATTTAAAAGAAAAGAA
* *
917031 GTTATAGCACCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGT
66 GTTATAGCACCAATAAAGTGTCGATACTTTATAAAAATGTAGCGATCCATAACAATATAACAAGT
* *
917096 AAAAAAATGACAAAATCGATTTCGAAATGATAAAA
131 AAAAAAATGACAAAATCGATCTCGAAATGACAAAA
917131 TCAGTAGTAA
Statistics
Matches: 154, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
168 154 1.00
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (168 bp):
GATATGTTGAAAGTGTCAATACTTTATTATAAGTATCGACACTTTTAGAATTTAAAAGAAAAGAA
GTTATAGCACCAATAAAGTGTCGATACTTTATAAAAATGTAGCGATCCATAACAATATAACAAGT
AAAAAAATGACAAAATCGATCTCGAAATGACAAAACCG
Found at i:924781 original size:2 final size:2
Alignment explanation
Indices: 924774--924801 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
924764 GTAGATCATA
924774 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
924802 CCAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:925278 original size:17 final size:18
Alignment explanation
Indices: 925256--925299 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
925246 ATCCCAAGCA
*
925256 ACCCCTCCA-CAAGTGTC
1 ACCCCTCAACCAAGTGTC
925273 ACCCCT-AATCCAAGTGTC
1 ACCCCTCAA-CCAAGTGTC
925291 ACCCCTCAA
1 ACCCCTCAA
925300 AAGTGCCATC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 1 0.04
17 6 0.26
18 14 0.61
19 2 0.09
ACGTcount: A:0.27, C:0.45, G:0.09, T:0.18
Consensus pattern (18 bp):
ACCCCTCAACCAAGTGTC
Done.