Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008225.1 Hibiscus syriacus cultivar Beakdansim tig00110858_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: 1890193
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 10
Found at i:852040 original size:26 final size:26
Alignment explanation
Indices: 852017--852070 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
852007 AAACATTAAT
*
852017 AAAATAATATACATATAAATATTATG
1 AAAATAATATACATAAAAATATTATG
*
852043 AAAATAATATATATAAAAAT-TT-TG
1 AAAATAATATACATAAAAATATTATG
852067 AAAA
1 AAAA
852071 GAAAGAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 6 0.23
25 2 0.08
26 18 0.69
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (26 bp):
AAAATAATATACATAAAAATATTATG
Found at i:852068 original size:24 final size:25
Alignment explanation
Indices: 852017--852087 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 25
852007 AAACATTAAT
*
852017 AAAATAATATACATATAAATATTATG
1 AAAATAATATA-ATATAAAAATTATG
*
852043 AAAATAATAT-ATATAAAAATTTTG
1 AAAATAATATAATATAAAAATTATG
* *
852067 AAAAGAA-AGAAT-TAAAAATTA
1 AAAATAATATAATATAAAAATTA
852088 AATATATGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
23 9 0.23
24 20 0.51
26 10 0.26
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (25 bp):
AAAATAATATAATATAAAAATTATG
Found at i:852560 original size:2 final size:2
Alignment explanation
Indices: 852553--852589 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
852543 TTTTAAGAAA
852553 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
852590 AATAAGATAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:855877 original size:2 final size:2
Alignment explanation
Indices: 855870--855897 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
855860 ATAATTAGTT
855870 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
855898 ACTAAAGAAT
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):
TA
Found at i:856198 original size:16 final size:16
Alignment explanation
Indices: 856173--856204 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
856163 TATATATATA
856173 TATATAATGAATTATT
1 TATATAATGAATTATT
*
856189 TATATTATGAATTATT
1 TATATAATGAATTATT
856205 AGATTTTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (16 bp):
TATATAATGAATTATT
Found at i:856800 original size:28 final size:28
Alignment explanation
Indices: 856768--856824 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
856758 GAGATATGGT
*
856768 ACATCAATACAGCAGGGTTGCATTATAA
1 ACATCAATACAGCAGGGTTGAATTATAA
*
856796 ACATCAATACAGCAGGTTTGAATTATAA
1 ACATCAATACAGCAGGGTTGAATTATAA
856824 A
1 A
856825 AATATGGCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (28 bp):
ACATCAATACAGCAGGGTTGAATTATAA
Found at i:865605 original size:70 final size:70
Alignment explanation
Indices: 865492--865626 Score: 225
Period size: 70 Copynumber: 1.9 Consensus size: 70
865482 CCCCTAAAAT
* *
865492 ATATTTAGAGCAATCAAAACGAATTAAATTATTTACAAAAATGATTAATCGGACTGAATAATTTT
1 ATATTTAGAACAATCAAAACGAATCAAATTATTTACAAAAATGATTAATCGGACTGAATAATTTT
865557 AACTA
66 AACTA
* * *
865562 ATATTTAGAATAATTAAAACGAATCAAATTATTTACAAAAATGATTAATCGGATTGAATAATTTT
1 ATATTTAGAACAATCAAAACGAATCAAATTATTTACAAAAATGATTAATCGGACTGAATAATTTT
865627 TATTAATTAG
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 60 1.00
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35
Consensus pattern (70 bp):
ATATTTAGAACAATCAAAACGAATCAAATTATTTACAAAAATGATTAATCGGACTGAATAATTTT
AACTA
Found at i:868222 original size:22 final size:22
Alignment explanation
Indices: 868194--868243 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
868184 TTAAATTAAG
868194 GCCATATGTCACAGCAAGGCCT
1 GCCATATGTCACAGCAAGGCCT
868216 GCCATATGTCACAGCAAGGCCT
1 GCCATATGTCACAGCAAGGCCT
868238 GCCATA
1 GCCATA
868244 CCTGGTTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.28, C:0.32, G:0.22, T:0.18
Consensus pattern (22 bp):
GCCATATGTCACAGCAAGGCCT
Found at i:873574 original size:29 final size:29
Alignment explanation
Indices: 873532--873717 Score: 171
Period size: 29 Copynumber: 6.3 Consensus size: 29
873522 ACTCGACCCA
873532 GTGACATTTTGGGAATTATTTTGAAAAAG
1 GTGACATTTTGGGAATTATTTTGAAAAAG
* *
873561 GTGATATTTTGGGAATTATTTTGAAAAAAAA
1 GTGACATTTTGGGAATTATTTTG--AAAAAG
* * *
873592 GTGACATTTTGGG--TTTTTTTTAAAAACA
1 GTGACATTTTGGGAATTATTTTGAAAAA-G
* * * *
873620 GTGACATTCTGGTAATTATTTTTAAAATG
1 GTGACATTTTGGGAATTATTTTGAAAAAG
* *
873649 ATGACATTTTGGGAATTA-TTTGTAAAATG
1 GTGACATTTTGGGAATTATTTTG-AAAAAG
* * *
873678 GTGATATTTTGGTAATTATTTTTAATAAAG
1 GTGACATTTTGGGAATTATTTTGAA-AAAG
*
873708 GTGAAATTTT
1 GTGACATTTT
873718 TGTAATTTTC
Statistics
Matches: 129, Mismatches: 20, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
27 5 0.04
28 15 0.12
29 66 0.51
30 26 0.20
31 17 0.13
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.44
Consensus pattern (29 bp):
GTGACATTTTGGGAATTATTTTGAAAAAG
Found at i:881123 original size:30 final size:29
Alignment explanation
Indices: 881027--881157 Score: 102
Period size: 30 Copynumber: 4.5 Consensus size: 29
881017 ACATTTTGGA
* * * * *
881027 AATTA-TTTTAAAAAGGTGACATTTTGAG
1 AATTATTTTTAAAAATGTAACAGTCTGGG
* *
881055 AATTATTTTGAAAAATGTAACATTCTGGG
1 AATTATTTTTAAAAATGTAACAGTCTGGG
* *
881084 AATTATTTTTAAAAATAGTGACAGTCTGGT
1 AATTATTTTTAAAAAT-GTAACAGTCTGGG
* * * * *
881114 AATTTTTTTTTAAAATGATGACATTTTGGG
1 AATTATTTTTAAAAATG-TAACAGTCTGGG
*
881144 AATTATTTGTAAAA
1 AATTATTTTTAAAA
881158 TGGTGATATT
Statistics
Matches: 83, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
28 5 0.06
29 34 0.41
30 44 0.53
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (29 bp):
AATTATTTTTAAAAATGTAACAGTCTGGG
Found at i:881176 original size:59 final size:57
Alignment explanation
Indices: 881014--881199 Score: 194
Period size: 59 Copynumber: 3.2 Consensus size: 57
881004 ACCCAACCCA
* * *
881014 GTGACATTTTGGAAATTATTTTAAAAAGGTGACATTTTGAG-AATTATTTTGAAAAAT
1 GTGACATTTTGGGAATTATTTTAAAATGGTGACATTTTG-GTAATTATTTTTAAAAAT
* * * * * * *
881071 GTAACATTCTGGGAATTATTTTTAAAAATAGTGACAGTCTGGTAATTTTTTTTTAAAAT
1 GTGACATTTTGGGAATTA-TTTT-AAAATGGTGACATTTTGGTAATTATTTTTAAAAAT
* *
881130 GATGACATTTTGGGAATTATTTGTAAAATGGTGATATTTTGGTAATTATTTTTAATAAAG
1 G-TGACATTTTGGGAATTATTT-TAAAATGGTGACATTTTGGTAATTATTTTTAA-AAAT
*
881190 GTGATATTTT
1 GTGACATTTT
881200 TGTAATTTTC
Statistics
Matches: 103, Mismatches: 20, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
57 15 0.15
58 5 0.05
59 63 0.61
60 20 0.19
ACGTcount: A:0.34, C:0.04, G:0.18, T:0.44
Consensus pattern (57 bp):
GTGACATTTTGGGAATTATTTTAAAATGGTGACATTTTGGTAATTATTTTTAAAAAT
Found at i:881195 original size:30 final size:29
Alignment explanation
Indices: 881014--881206 Score: 174
Period size: 29 Copynumber: 6.6 Consensus size: 29
881004 ACCCAACCCA
*
881014 GTGACATTTTGGAAATTA-TTTTAAAAAG
1 GTGACATTTTGGTAATTATTTTTAAAAAG
* *
881042 GTGACATTTTGAG-AATTATTTTGAAAAAT
1 GTGACATTTTG-GTAATTATTTTTAAAAAG
* * * *
881071 GTAACATTCTGGGAATTATTTTTAAAAATA
1 GTGACATTTTGGTAATTATTTTTAAAAA-G
* * * *
881101 GTGACAGTCTGGTAATTTTTTTTTAAAATG
1 GTGACATTTTGGTAA-TTATTTTTAAAAAG
* * * *
881131 ATGACATTTTGGGAATTATTTGTAAAATG
1 GTGACATTTTGGTAATTATTTTTAAAAAG
*
881160 GTGATATTTTGGTAATTATTTTTAATAAAG
1 GTGACATTTTGGTAATTATTTTTAA-AAAG
* *
881190 GTGATATTTTTGTAATT
1 GTGACATTTTGGTAATT
881207 TTCGAATGTG
Statistics
Matches: 135, Mismatches: 24, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
28 17 0.13
29 65 0.48
30 42 0.31
31 11 0.08
ACGTcount: A:0.34, C:0.04, G:0.18, T:0.45
Consensus pattern (29 bp):
GTGACATTTTGGTAATTATTTTTAAAAAG
Found at i:885197 original size:20 final size:19
Alignment explanation
Indices: 885146--885202 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
885136 AACCAATAAT
885146 AATAAACATAAAAT-AATTG
1 AATAAA-ATAAAATAAATTG
* *
885165 GATGAAAAAAAAATGAAATTG
1 AAT-AAAATAAAAT-AAATTG
885186 AATAAAATAAAATAAAT
1 AATAAAATAAAATAAAT
885203 GAAGATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 12 0.39
20 12 0.39
21 7 0.23
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.23
Consensus pattern (19 bp):
AATAAAATAAAATAAATTG
Found at i:885310 original size:21 final size:20
Alignment explanation
Indices: 885286--885345 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 20
885276 ACAAAGAAAC
885286 TAAAAATATAATGAAAATAAA
1 TAAAAATATAAT-AAAATAAA
*
885307 TAAATAGTATAAATAAAAT-AA
1 TAAA-AATAT-AATAAAATAAA
885328 TAAAATATATATATAAAA
1 TAAAA-ATATA-ATAAAA
885346 ATATATGTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
20 2 0.06
21 19 0.58
22 9 0.27
23 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.28
Consensus pattern (20 bp):
TAAAAATATAATAAAATAAA
Found at i:885318 original size:22 final size:21
Alignment explanation
Indices: 885292--885398 Score: 76
Period size: 22 Copynumber: 4.9 Consensus size: 21
885282 AAACTAAAAA
885292 TATAATGAAAATAAATAAATAG
1 TATAAT-AAAATAAATAAATAG
885314 TATAAATAAAAT-AATAAAATA-
1 TAT-AATAAAATAAAT-AAATAG
* ** *
885335 TATATATAAAAATATATGTATAA
1 TATA-AT-AAAATAAATAAATAG
* *
885358 TGTAATAAAAT-ACTAAATAG
1 TATAATAAAATAAATAAATAG
885378 TAATAATAATAATAAATAAAT
1 T-ATAATAA-AATAAATAAAT
885399 GAAAAATTAA
Statistics
Matches: 65, Mismatches: 11, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
20 6 0.09
21 19 0.29
22 26 0.40
23 14 0.22
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.32
Consensus pattern (21 bp):
TATAATAAAATAAATAAATAG
Found at i:885393 original size:19 final size:18
Alignment explanation
Indices: 885359--885395 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
885349 TATGTATAAT
*
885359 GTAATAAAATACTAAATA
1 GTAATAAAATAATAAATA
885377 GTAATAATAATAATAAATA
1 GTAATAA-AATAATAAATA
885396 AATGAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (18 bp):
GTAATAAAATAATAAATA
Found at i:885638 original size:23 final size:23
Alignment explanation
Indices: 885604--885650 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
885594 ACGCAAAGAA
885604 AAATGAAAAAAATTATAA-TAAAT
1 AAATGAAAAAAA-TATAATTAAAT
885627 AAAT-AAATAAAATATAATTAAAT
1 AAATGAAA-AAAATATAATTAAAT
885650 A
1 A
885651 TATACATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (23 bp):
AAATGAAAAAAATATAATTAAAT
Found at i:885661 original size:8 final size:8
Alignment explanation
Indices: 885648--885676 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
885638 ATATAATTAA
885648 ATATATAC
1 ATATATAC
885656 ATATATAC
1 ATATATAC
885664 ATATATAC
1 ATATATAC
885672 ATATA
1 ATATA
885677 AATAATAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATATAC
Found at i:886168 original size:37 final size:37
Alignment explanation
Indices: 886075--886178 Score: 154
Period size: 37 Copynumber: 2.8 Consensus size: 37
886065 ATGCTTGTGG
* * ** *
886075 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
*
886112 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
886149 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
886179 GGACTAAAAG
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
Found at i:887058 original size:106 final size:106
Alignment explanation
Indices: 886922--888197 Score: 2003
Period size: 106 Copynumber: 12.0 Consensus size: 106
886912 ACATTGTTCT
* * * *
886922 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * *
886987 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
887028 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCCGAAATTAGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * *
887093 CCAGCGGTCCCATCGTCGTGAAGTTGAACTTACGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
887134 GAGTCCAATATCCTTCGCTATGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
887199 CCGGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
887240 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
887305 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
887346 GAGTCCAATATCCTTCGCTGTGAAATTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
887411 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * *
887452 GAGTCCAATATATTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
887517 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
887558 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
887623 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
887664 GAGTCCAATATTCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
887729 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
887770 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
887835 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
887876 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
887941 CCAGCTGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
887982 GAGTCTAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
888047 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
888088 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTAGCTCTGAATTTAGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * *
888153 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
888194 GAGT
1 GAGT
888198 GGCACGATAT
Statistics
Matches: 1077, Mismatches: 93, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 1077 1.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:889851 original size:16 final size:15
Alignment explanation
Indices: 889807--889854 Score: 57
Period size: 13 Copynumber: 3.3 Consensus size: 15
889797 TTCTTTTTGA
889807 TTTTTGTTA-TTTCT
1 TTTTTGTTATTTTCT
*
889821 TTTTT-TT-TCTTCT
1 TTTTTGTTATTTTCT
889834 TTTTTGCTTATTTTCT
1 TTTTTG-TTATTTTCT
889850 TTTTT
1 TTTTT
889855 CGTTTTGCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 11 0.39
14 5 0.18
15 2 0.07
16 10 0.36
ACGTcount: A:0.04, C:0.10, G:0.04, T:0.81
Consensus pattern (15 bp):
TTTTTGTTATTTTCT
Found at i:894138 original size:22 final size:21
Alignment explanation
Indices: 894099--894156 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
894089 TTGGATGAAA
**
894099 AAAAAATGAAATTGAATAAAT
1 AAAAAATGAAATAAAATAAAT
*
894120 AAAAAATGAAGATAAAATATAT
1 AAAAAATGAA-ATAAAATAAAT
894142 ACAAAAA-G-AATAAAA
1 A-AAAAATGAAATAAAA
894157 AAGGTAAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 6 0.19
21 11 0.34
22 10 0.31
23 5 0.16
ACGTcount: A:0.71, C:0.02, G:0.09, T:0.19
Consensus pattern (21 bp):
AAAAAATGAAATAAAATAAAT
Found at i:894489 original size:33 final size:32
Alignment explanation
Indices: 894452--894576 Score: 89
Period size: 32 Copynumber: 3.9 Consensus size: 32
894442 CATAGATTAA
894452 AAAAAATATATAATATATATATAATAATAATAG
1 AAAAAATATATAATATATATA-AATAATAATAG
*** * *
894485 -AAAAATAATATAATATACGCAAAGAAAAAT-G
1 AAAAAAT-ATATAATATATATAAATAATAATAG
* *
894516 AAAAAAAATATAATA-A-ATAAATAAATAAATAT
1 AAAAAATATATAATATATATAAAT-AAT-AATAG
* *
894548 AATTAAATATAT-ATATATATATATAATAA
1 AA-AAAATATATAATATATATAAATAATAA
894577 GGATTAAATT
Statistics
Matches: 70, Mismatches: 14, Indels: 17
0.69 0.14 0.17
Matches are distributed among these distances:
29 3 0.04
30 3 0.04
31 12 0.17
32 25 0.36
33 22 0.31
34 5 0.07
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.30
Consensus pattern (32 bp):
AAAAAATATATAATATATATAAATAATAATAG
Found at i:894554 original size:18 final size:18
Alignment explanation
Indices: 894528--894576 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
894518 AAAAAATATA
894528 ATAAATAAATAAATAAAT
1 ATAAATAAATAAATAAAT
* * *
894546 ATAATTAAATATATATAT
1 ATAAATAAATAAATAAAT
*
894564 ATATATATAATAA
1 ATAAATA-AATAA
894577 GGATTAAATT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAAATAAATAAATAAAT
Found at i:895009 original size:37 final size:37
Alignment explanation
Indices: 894968--895060 Score: 114
Period size: 37 Copynumber: 2.5 Consensus size: 37
894958 ATGCTTGTTG
* * *
894968 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
* ** *
895005 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
*
895042 ATCCTATTTTTAAGAGTTT
1 ATCCTATTTTTAGGAGTTT
895061 GAATCCTAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATAATAGCAAAACTCT
Found at i:895854 original size:21 final size:21
Alignment explanation
Indices: 895825--895877 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
895815 ATTCTGACTA
895825 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
895846 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
895867 TCGCAATGCGA
1 TCGCATTGCGA
895878 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:895909 original size:20 final size:20
Alignment explanation
Indices: 895899--895952 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
895889 GCAATGCGAA
895899 TCTGACTATCGCAACGAGAT
1 TCTGACTATCGCAACGAGAT
* *
895919 TTTGACTATTGCAACGAGAT
1 TCTGACTATCGCAACGAGAT
895939 TCTGACTATCGCAA
1 TCTGACTATCGCAA
895953 TACTGAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (20 bp):
TCTGACTATCGCAACGAGAT
Found at i:899280 original size:20 final size:20
Alignment explanation
Indices: 899255--899423 Score: 259
Period size: 20 Copynumber: 8.4 Consensus size: 20
899245 CAACGCGGAA
899255 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAAT-TGACT
* *
899275 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAATTGACT
*
899295 ATCGCAATGCGGAATTGACT
1 ATCGCAACGCGGAATTGACT
*
899315 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAATTGACT
*
899335 ATCGCAACGTGGAATTGACT
1 ATCGCAACGCGGAATTGACT
* *
899355 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGGAATTGACT
899375 ATCGCAACGCGGAATTGACT
1 ATCGCAACGCGGAATTGACT
899395 ATCGCAACGCGGAATTGACT
1 ATCGCAACGCGGAATTGACT
899415 ATCGCAACG
1 ATCGCAACG
899424 AGAGAATCGC
Statistics
Matches: 134, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
20 131 0.98
21 3 0.02
ACGTcount: A:0.34, C:0.24, G:0.23, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGGAATTGACT
Found at i:899453 original size:34 final size:34
Alignment explanation
Indices: 899415--899491 Score: 120
Period size: 34 Copynumber: 2.3 Consensus size: 34
899405 GGAATTGACT
*
899415 ATCGCAACGAGAGAATCGCAATGC-GAAATGAAAA
1 ATCGCAACGAGAGAATCGCAATGCAAAAATG-AAA
*
899449 ATCGCAACGAGTGAATCGCAATGCAAAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCAAAAATGAAA
899483 ATCGCAACG
1 ATCGCAACG
899492 CGAATTTAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
34 35 0.88
35 5 0.12
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (34 bp):
ATCGCAACGAGAGAATCGCAATGCAAAAATGAAA
Found at i:899549 original size:34 final size:34
Alignment explanation
Indices: 899506--899591 Score: 120
Period size: 34 Copynumber: 2.5 Consensus size: 34
899496 TTTAGTTTCA
*
899506 CGTTGCGATTTTCATTTTCGCA-TTGCGATTCTTT
1 CGTTGCGATTTTCA-TTTCGCATTTGCGATTCTCT
*
899540 CGTTGCGATTTTCATTTCGCATTTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTTGCGATTCTCT
**
899574 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
899592 TGTGTTGCGA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
33 7 0.15
34 40 0.85
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.48
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTCGCATTTGCGATTCTCT
Found at i:899727 original size:14 final size:14
Alignment explanation
Indices: 899708--899744 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
899698 CATCAATTAA
899708 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
899722 ACAAATCATCTTTT
1 ACAAATCAACATTT
899736 ACAAATCAA
1 ACAAATCAA
899745 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:901210 original size:42 final size:42
Alignment explanation
Indices: 901131--901223 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
901121 CCTCTTCAAC
* * *
901131 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
901173 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
901215 GATGACAGG
1 GATGACAGG
901224 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:901726 original size:20 final size:20
Alignment explanation
Indices: 901703--901831 Score: 143
Period size: 20 Copynumber: 6.5 Consensus size: 20
901693 GAAACTTAAA
*
901703 ATCGCAACGCGAAAATGACC
1 ATCGCAACGCGAAAATGACT
901723 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
901743 ATCGCAACGTGAAAATGAAT
1 ATCGCAACGCGAAAATGACT
*
901763 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* ** *
901783 ATCGCAATGCGAATTTAACT
1 ATCGCAACGCGAAAATGACT
* * *
901803 ATCGCAATGC-AAATTTAACT
1 ATCGCAACGCGAAA-ATGACT
901823 ATCGCAACG
1 ATCGCAACG
901832 AGAGAATCGC
Statistics
Matches: 97, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
19 2 0.02
20 95 0.98
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:901913 original size:20 final size:20
Alignment explanation
Indices: 901890--901942 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
901880 GATAATCAAA
901890 TTCGCATTGTGATAGTCATT
1 TTCGCATTGTGATAGTCATT
*
901910 TTCGCATTGCGATAGTCATT
1 TTCGCATTGTGATAGTCATT
*
901930 TTCGCGTTGTGAT
1 TTCGCATTGTGAT
901943 TTTATTGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.43
Consensus pattern (20 bp):
TTCGCATTGTGATAGTCATT
Found at i:902006 original size:20 final size:20
Alignment explanation
Indices: 901981--902018 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
901971 GCAATTCTCT
*
901981 CGTTGCGATAGTCATTTTCG
1 CGTTGCAATAGTCATTTTCG
902001 CGTTGCAATAGTCATTTT
1 CGTTGCAATAGTCATTTT
902019 TGCATTGTGA
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:0.18, C:0.18, G:0.21, T:0.42
Consensus pattern (20 bp):
CGTTGCAATAGTCATTTTCG
Found at i:902007 original size:34 final size:34
Alignment explanation
Indices: 901916--902009 Score: 109
Period size: 33 Copynumber: 2.8 Consensus size: 34
901906 CATTTTCGCA
** * *
901916 TTGCGATAGTCATTTTCGCGTTGTGATTTTATTG
1 TTGCGATAGTCATTTTCGCGTTGCAATTCTATCG
** * *
901950 TTGCGATTTTCA-TTTCGCATTGCAATTCTCTCG
1 TTGCGATAGTCATTTTCGCGTTGCAATTCTATCG
901983 TTGCGATAGTCATTTTCGCGTTGCAAT
1 TTGCGATAGTCATTTTCGCGTTGCAAT
902010 AGTCATTTTT
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
33 25 0.52
34 23 0.48
ACGTcount: A:0.16, C:0.18, G:0.20, T:0.46
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCGTTGCAATTCTATCG
Found at i:903642 original size:20 final size:20
Alignment explanation
Indices: 903617--903656 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
903607 TTGAAACTTT
903617 AAATCGCAACACAAAAATGA
1 AAATCGCAACACAAAAATGA
*
903637 AAATCGCAACACGAAAATGA
1 AAATCGCAACACAAAAATGA
903657 CTATCACAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.20, G:0.12, T:0.10
Consensus pattern (20 bp):
AAATCGCAACACAAAAATGA
Found at i:903666 original size:20 final size:20
Alignment explanation
Indices: 903617--903666 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
903607 TTGAAACTTT
*
903617 AAATCGCAACACAAAAATGA
1 AAATCACAACACAAAAATGA
* *
903637 AAATCGCAACACGAAAATGA
1 AAATCACAACACAAAAATGA
**
903657 CTATCACAAC
1 AAATCACAAC
903667 GCAAGAATCG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.54, C:0.24, G:0.10, T:0.12
Consensus pattern (20 bp):
AAATCACAACACAAAAATGA
Found at i:903700 original size:33 final size:34
Alignment explanation
Indices: 903638--903711 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 34
903628 CAAAAATGAA
**
903638 AATCGCAACACGAAAATGACTATCACAACG-CAAG
1 AATCGCAACACGAAAATGAAAATCACAACGAC-AG
* *
903672 AATCGCAACGCG-AAATGAAAATCGCAACGACAG
1 AATCGCAACACGAAAATGAAAATCACAACGACAG
903705 AATCGCA
1 AATCGCA
903712 TTGCGATAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
33 23 0.66
34 12 0.34
ACGTcount: A:0.46, C:0.26, G:0.18, T:0.11
Consensus pattern (34 bp):
AATCGCAACACGAAAATGAAAATCACAACGACAG
Found at i:904343 original size:21 final size:21
Alignment explanation
Indices: 904319--904364 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
904309 TATTCGCATT
*
904319 GCGAATTAGGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
* *
904340 GCGAATTTCGAAAATCGCAAT
1 GCGAATTACGAAAATCGCAAC
904361 GCGA
1 GCGA
904365 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (21 bp):
GCGAATTACGAAAATCGCAAC
Found at i:916006 original size:399 final size:399
Alignment explanation
Indices: 915264--916062 Score: 1573
Period size: 400 Copynumber: 2.0 Consensus size: 399
915254 TCCTTTAGGA
915264 TCATGATATAAACGCGCATTTAAAGCGGTGAAACGTGAAAAACTGAAAACCATCAAGAGTCGCGC
1 TCATGATATAAACGCGCATTTAAAGCGGTGAAACGTGAAAAACTGAAAACCATCAAGAGTCGCGC
915329 ATGCTCATCGTTTTGAAGCTATAGAAAATCGACAAGATGTGGCCGCAAGTTGCAAATAACCCAAT
66 ATGCTCATCGTTTTGAAGCTATAGAAAATCGACAAGATGTGGCCGCAAGTTGCAAATAACCCAAT
915394 GATCACTGGGTATTGTTTTACATACAAATTTTTGTCAGGAACTGAGAAAACCAAATTGATTTTTT
131 GATCACTGGGTATTGTTTTACATACAAATTTTTGTCAGGAACTGAGAAAACCAAATTGATTTTTT
915459 CCCCGAGAGTAATGTTATCATAGAGGTTTATGGCTGAGCTGTGTTTGTAAAGTATATATATTATT
196 CCCCGAGAGTAATGTTATCATAGAGGTTTATGGCTGAGCTGTGTTTGTAAAGTATATATATTATT
915524 AATAATTAAAAAAATTATGAATAGATATTATTTTATAATCATATCTTATATTATTAAAATAAATT
261 AATAATTAAAAAAATTATGAATAGATATTATTTTATAATCATATCTTATATTATTAAAATAAATT
915589 CAAAGACCAATAAAAAAAAGAGGACTCAAAATTTATTTGAGAAGAATTTTCAAATATAAGAAAAC
326 CAAAGACCAATAAAAAAAAGAGGACTCAAAATTTATTTGAGAAGAATTTTCAAATATAAGAAAAC
915654 TATTTTATT
391 TATTTTATT
915663 TCATGATATAAACGCGCATTTAAAGCGGTGAAACGTGAAAAACTGAAAACCATCAAGAGTCGCGC
1 TCATGATATAAACGCGCATTTAAAGCGGTGAAACGTGAAAAACTGAAAACCATCAAGAGTCGCGC
915728 ATGCTCATCGTTTTGAAGCTATAGAAAATCGACAAGATGTGGCCGCAAGTTGCAAATAATCCCAA
66 ATGCTCATCGTTTTGAAGCTATAGAAAATCGACAAGATGTGGCCGCAAGTTGCAAATAA-CCCAA
915793 TGATCACTGGGTATTGTTTTACATACAAA-TTTTGTCAGGAACTGAGAAAACCAAATTGATTTTT
130 TGATCACTGGGTATTGTTTTACATACAAATTTTTGTCAGGAACTGAGAAAACCAAATTGA-TTTT
915857 TTCCCCGAGAGTAATGTTATCATAGAGGTTTATGGCTGAGCTGTGTTTGTAAAGTATATATATTA
194 TTCCCCGAGAGTAATGTTATCATAGAGGTTTATGGCTGAGCTGTGTTTGTAAAGTATATATATTA
915922 TTAATAATTAAAAAAATTATGAATAGATATTATTTTATAATCATATCTTATATTATTAAAATAAA
259 TTAATAATTAAAAAAATTATGAATAGATATTATTTTATAATCATATCTTATATTATTAAAATAAA
915987 TTCAAAGACCAATAAAAAAAAGAGGACTCAAAATTTATTTGAGAAGAATTTTCAAATATAAGAAA
324 TTCAAAGACCAATAAAAAAAAGAGGACTCAAAATTTATTTGAGAAGAATTTTCAAATATAAGAAA
916052 ACTATTTTATT
389 ACTATTTTATT
916063 CTGAAGGCTT
Statistics
Matches: 398, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
399 154 0.39
400 244 0.61
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.32
Consensus pattern (399 bp):
TCATGATATAAACGCGCATTTAAAGCGGTGAAACGTGAAAAACTGAAAACCATCAAGAGTCGCGC
ATGCTCATCGTTTTGAAGCTATAGAAAATCGACAAGATGTGGCCGCAAGTTGCAAATAACCCAAT
GATCACTGGGTATTGTTTTACATACAAATTTTTGTCAGGAACTGAGAAAACCAAATTGATTTTTT
CCCCGAGAGTAATGTTATCATAGAGGTTTATGGCTGAGCTGTGTTTGTAAAGTATATATATTATT
AATAATTAAAAAAATTATGAATAGATATTATTTTATAATCATATCTTATATTATTAAAATAAATT
CAAAGACCAATAAAAAAAAGAGGACTCAAAATTTATTTGAGAAGAATTTTCAAATATAAGAAAAC
TATTTTATT
Found at i:919592 original size:192 final size:197
Alignment explanation
Indices: 919265--919654 Score: 745
Period size: 192 Copynumber: 2.0 Consensus size: 197
919255 TTAGAATTGA
919265 TCTAGTGACTATTTTAATAGAAGCTTTGATGGTGTGCATTGAACAGAAAAACAGCAAGTGGCTGT
1 TCTAGTGACTATTTTAATAGAAGCTTTGATGGTGTGCATTGAACAGAAAAACAGCAAGTGGCTGT
919330 ACGGAAATGGGTCGTTATTCGTCAATCTTTTCCCAGCTAATTTCTTATGTATTTGACTTCTGAAA
66 ACGGAAATGGGTCGTTATTCGTCAATCTTTTCCCAGCTAATTTCTTATGTATTTGACTTCTGAAA
919395 ATGAGTTTTTAATTCTTTCATC-AAAT-ACAAGACCATG-AC-GTAAG-AAATAGAATCATGAGT
131 ATGAGTTTTTAATTCTTTCATCAAAATAACAAGACCATGAACAGTAAGAAAATAGAATCATGAGT
919455 TT
196 TT
919457 TCTAGTGACTATTTTAATAGAAGCTTTGATGGTGTGCATTGAACAGAAAAACAGCAAGTGGCTGT
1 TCTAGTGACTATTTTAATAGAAGCTTTGATGGTGTGCATTGAACAGAAAAACAGCAAGTGGCTGT
919522 ACGGAAATGGGTCGTTATTCGTCAATCTTTTCCCAGCTAATTTCTTATGTATTTGACTTCTGAAA
66 ACGGAAATGGGTCGTTATTCGTCAATCTTTTCCCAGCTAATTTCTTATGTATTTGACTTCTGAAA
919587 ATGAGTTTTTAATTCTTTCATCAAAATAACAAGACCATGAACAGTAAGAAAATAGAATCATGAGT
131 ATGAGTTTTTAATTCTTTCATCAAAATAACAAGACCATGAACAGTAAGAAAATAGAATCATGAGT
919652 TT
196 TT
919654 T
1 T
919655 AGTTTTCTTC
Statistics
Matches: 193, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
192 152 0.79
193 4 0.02
194 11 0.06
195 2 0.01
196 5 0.03
197 19 0.10
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (197 bp):
TCTAGTGACTATTTTAATAGAAGCTTTGATGGTGTGCATTGAACAGAAAAACAGCAAGTGGCTGT
ACGGAAATGGGTCGTTATTCGTCAATCTTTTCCCAGCTAATTTCTTATGTATTTGACTTCTGAAA
ATGAGTTTTTAATTCTTTCATCAAAATAACAAGACCATGAACAGTAAGAAAATAGAATCATGAGT
TT
Found at i:921216 original size:22 final size:23
Alignment explanation
Indices: 921188--921249 Score: 99
Period size: 22 Copynumber: 2.7 Consensus size: 23
921178 ACTTTACAAC
921188 TACCTATTACATTATATAA-CGA
1 TACCTATTACATTATATAAGCGA
*
921210 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAGCGA
*
921233 TACCTATTACATCATAT
1 TACCTATTACATTATAT
921250 TTTACCTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
22 19 0.51
23 18 0.49
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAGCGA
Found at i:928063 original size:21 final size:21
Alignment explanation
Indices: 928011--928105 Score: 88
Period size: 21 Copynumber: 4.6 Consensus size: 21
928001 CAACCCAAGT
*
928011 TCCAAATTCGCAACGCGAAAG
1 TCCAAATTCGCAACGCGATAG
* *
928032 TCGAGATTCGCAACGCGATAG
1 TCCAAATTCGCAACGCGATAG
* *
928053 TCCAAAATCGCAAAGCGAT--
1 TCCAAATTCGCAACGCGATAG
* *
928072 T-TAAGATTCGCAACGCGATAC
1 TCCAA-ATTCGCAACGCGATAG
*
928093 TCCAAAATCGCAA
1 TCCAAATTCGCAA
928106 TGCATTTGTT
Statistics
Matches: 58, Mismatches: 12, Indels: 8
0.74 0.15 0.10
Matches are distributed among these distances:
18 2 0.03
19 13 0.22
21 41 0.71
22 2 0.03
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (21 bp):
TCCAAATTCGCAACGCGATAG
Found at i:929803 original size:28 final size:30
Alignment explanation
Indices: 929762--929818 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
929752 GATAGTATCA
929762 TAAAATGTCACATTA-ATATTATT-TTAGAG
1 TAAAATGTCACATTAGATATT-TTATTAGAG
929791 TAAAA-GTCACATTAGATATTTTATTAGA
1 TAAAATGTCACATTAGATATTTTATTAGA
929819 TAGTCATGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 11 0.42
29 15 0.58
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (30 bp):
TAAAATGTCACATTAGATATTTTATTAGAG
Found at i:931446 original size:25 final size:25
Alignment explanation
Indices: 931418--931466 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
931408 TTTATTTTCT
931418 TTTTCTATAAAATTCTT-TAAATTTA
1 TTTTCTATAAAATT-TTATAAATTTA
*
931443 TTTTCTCTAAAATTTTATAAATTT
1 TTTTCTATAAAATTTTATAAATTT
931467 TAAATTAAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (25 bp):
TTTTCTATAAAATTTTATAAATTTA
Found at i:931787 original size:17 final size:18
Alignment explanation
Indices: 931765--931804 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
931755 ACATAATTTT
931765 TAAAACAT-AAAGTTAAA
1 TAAAACATCAAAGTTAAA
*
931782 TAAAACATCAATGTTAAA
1 TAAAACATCAAAGTTAAA
931800 TAAAA
1 TAAAA
931805 GTCATTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.25
Consensus pattern (18 bp):
TAAAACATCAAAGTTAAA
Found at i:933602 original size:26 final size:26
Alignment explanation
Indices: 933551--933603 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
933541 ATGATGCACG
*
933551 ATAATTTATATATTCATTTACAAAAT
1 ATAATTTATATATTCATATACAAAAT
933577 ATAATTTATCATA-TCATAT-CATAAAT
1 ATAATTTAT-ATATTCATATACA-AAAT
933603 A
1 A
933604 CTTTAAAGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 2 0.08
26 19 0.79
27 3 0.12
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.43
Consensus pattern (26 bp):
ATAATTTATATATTCATATACAAAAT
Found at i:951536 original size:2 final size:2
Alignment explanation
Indices: 951529--951554 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
951519 ACCCCTCTTC
951529 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
951555 TACATCTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:952826 original size:66 final size:66
Alignment explanation
Indices: 952720--952874 Score: 265
Period size: 66 Copynumber: 2.3 Consensus size: 66
952710 ATCAGTACTC
* * * *
952720 TATGTTGAGTATTAATACTCAGGTATATGTATCCGTATCGGTGTGATAGTATCTTTATAGGTACC
1 TATGTTGAGTATTGATACTCAGGTATATGTATCCATATCGGTGTGACAATATCTTTATAGGTACC
952785 A
66 A
952786 TATGTTGAGTATTGATACTCAGGTATATGTATCCATATCGGTGTGACAATATCTTTATAGGTACC
1 TATGTTGAGTATTGATACTCAGGTATATGTATCCATATCGGTGTGACAATATCTTTATAGGTACC
952851 A
66 A
*
952852 TATGTTGAGTATTGATATTCAGG
1 TATGTTGAGTATTGATACTCAGG
952875 CATAACAACC
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 84 1.00
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (66 bp):
TATGTTGAGTATTGATACTCAGGTATATGTATCCATATCGGTGTGACAATATCTTTATAGGTACC
A
Found at i:959805 original size:2 final size:2
Alignment explanation
Indices: 959798--959826 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
959788 TATTACATGT
959798 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
959827 GAATATGCTA
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:961677 original size:14 final size:14
Alignment explanation
Indices: 961655--961690 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
961645 ATTACATTGT
*
961655 ATTTACATCTTCGC
1 ATTTGCATCTTCGC
961669 ATTTGCATCTTCGC
1 ATTTGCATCTTCGC
961683 ATTTGCAT
1 ATTTGCAT
961691 AATCATTATG
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:0.19, C:0.25, G:0.11, T:0.44
Consensus pattern (14 bp):
ATTTGCATCTTCGC
Found at i:962730 original size:26 final size:27
Alignment explanation
Indices: 962701--962768 Score: 66
Period size: 28 Copynumber: 2.5 Consensus size: 27
962691 AATCGATACC
*
962701 TTTTGCATTTGCATTTGCA-TTCACAT
1 TTTTGCATTTGCATTTACATTTCACAT
* * * **
962727 TTTTACGTTTGTATTTACATTTTCATTT
1 TTTTGCATTTGCATTTACA-TTTCACAT
962755 TTTTGCATTTGCAT
1 TTTTGCATTTGCAT
962769 ATTTGCATAG
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
26 15 0.48
28 16 0.52
ACGTcount: A:0.18, C:0.15, G:0.10, T:0.57
Consensus pattern (27 bp):
TTTTGCATTTGCATTTACATTTCACAT
Found at i:965185 original size:1 final size:1
Alignment explanation
Indices: 965174--965282 Score: 83
Period size: 1 Copynumber: 109.0 Consensus size: 1
965164 CTCATCCATC
* * * * *** * *
965174 AAAAAAGAAAAAGAAGAAAAAAAGAAAAAAAAAGCGAAAAAAAAGAAAAAAAAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * *
965239 AAAGAAAAAAAAAAAAAAAAGAAAAGAAAAGAAATAAAATAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
965283 TTGAATCAAG
Statistics
Matches: 80, Mismatches: 28, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 80 1.00
ACGTcount: A:0.86, C:0.01, G:0.11, T:0.02
Consensus pattern (1 bp):
A
Found at i:965193 original size:8 final size:8
Alignment explanation
Indices: 965174--965268 Score: 104
Period size: 8 Copynumber: 11.4 Consensus size: 8
965164 CTCATCCATC
965174 AAAAAAGA
1 AAAAAAGA
965182 AAAAGAAGA
1 AAAA-AAGA
965191 AAAAAAGAAA
1 AAAAAAG--A
965201 AAAAAAGCGAA
1 AAAAAA--G-A
965212 AAAAAAGA
1 AAAAAAGA
*
965220 AAAAAAAA
1 AAAAAAGA
965228 AAAAAAGA
1 AAAAAAGA
965236 AAAAAAGA
1 AAAAAAGA
965244 AAAAAA-A
1 AAAAAAGA
965251 AAAAAA-A
1 AAAAAAGA
*
965258 AGAAAAGA
1 AAAAAAGA
965266 AAA
1 AAA
965269 GAAATAAAAT
Statistics
Matches: 77, Mismatches: 4, Indels: 12
0.83 0.04 0.13
Matches are distributed among these distances:
7 13 0.17
8 39 0.51
9 9 0.12
10 7 0.09
11 8 0.10
12 1 0.01
ACGTcount: A:0.87, C:0.01, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:965197 original size:11 final size:10
Alignment explanation
Indices: 965176--965277 Score: 107
Period size: 10 Copynumber: 9.7 Consensus size: 10
965166 CATCCATCAA
965176 AAAAGAAAAAG
1 AAAA-AAAAAG
965187 AAGAAAAAAAG
1 AA-AAAAAAAG
965198 AAAAAAAAAG
1 AAAAAAAAAG
*
965208 CGAAAAAAAAG
1 -AAAAAAAAAG
965219 AAAAAAAAA-
1 AAAAAAAAAG
*
965228 AAAAAAGAAAA
1 AAAAAA-AAAG
*
965239 AAAGAAAAAAA
1 AAA-AAAAAAG
965250 AAAAAAAAAG
1 AAAAAAAAAG
*
965260 AAAAGAAAAG
1 AAAAAAAAAG
965270 AAATAAAA
1 AAA-AAAA
965278 TAAAATTGAA
Statistics
Matches: 80, Mismatches: 5, Indels: 12
0.82 0.05 0.12
Matches are distributed among these distances:
9 6 0.08
10 37 0.46
11 32 0.40
12 5 0.06
ACGTcount: A:0.86, C:0.01, G:0.12, T:0.01
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:965226 original size:25 final size:25
Alignment explanation
Indices: 965174--965282 Score: 130
Period size: 27 Copynumber: 4.2 Consensus size: 25
965164 CTCATCCATC
*
965174 AAAAAAGAAAAAGAAGAAAAAAAGAAA
1 AAAAAAGAAAAAAAAG-AAAAAA-AAA
965201 AAAAAAGCGAAAAAAAAGAAAAAAAAA
1 AAAAAA--GAAAAAAAAGAAAAAAAAA
965228 AAAAAAG-AAAAAAAGAAAAAAAAAA
1 AAAAAAGAAAAAAAAG-AAAAAAAAA
* *
965253 AAAAAAGAAAAGAAAAGAAATAAAAT
1 AAAAAAGAAAA-AAAAGAAAAAAAAA
965279 AAAA
1 AAAA
965283 TTGAATCAAG
Statistics
Matches: 74, Mismatches: 3, Indels: 11
0.84 0.03 0.12
Matches are distributed among these distances:
24 8 0.11
25 17 0.23
26 14 0.19
27 20 0.27
28 6 0.08
29 9 0.12
ACGTcount: A:0.86, C:0.01, G:0.11, T:0.02
Consensus pattern (25 bp):
AAAAAAGAAAAAAAAGAAAAAAAAA
Found at i:966847 original size:28 final size:28
Alignment explanation
Indices: 966807--966862 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
966797 ATCCAAGTGG
966807 GGCATCTTGAAGGCTCACA-TCAGCATGA
1 GGCATCTTGAAGGCTCACACT-AGCATGA
966835 GGCATCTTGAAGGCTCACACTAGCATGA
1 GGCATCTTGAAGGCTCACACTAGCATGA
966863 AAAGGTTGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 26 0.96
29 1 0.04
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.21
Consensus pattern (28 bp):
GGCATCTTGAAGGCTCACACTAGCATGA
Found at i:968211 original size:40 final size:40
Alignment explanation
Indices: 968155--968641 Score: 796
Period size: 40 Copynumber: 12.2 Consensus size: 40
968145 ATATAGAGGA
*
968155 TTTATCTCACTGAAGATTGTTTTTCCTTGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
*
968195 TTTATCTCATTCAAGATTGTTTTTCCTTGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
* * *
968235 TTTATTTCATTCAAGATTGTTTTTCCTCGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
* * *
968275 TTTATTTCATTCAAGATTGTTTTTCCTTGAAACAAAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
968315 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
*
968355 TTTATCTCACTCAAGATTGTTTTTTCTTGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
*
968395 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACATAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
* *
968435 TTTATCTCGCTCAAGATT-ATTTTCCTTGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
*
968474 TTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
* *
968514 TTTATCTCGCTCAAGATTGTTTTTCCCTGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
*
968554 TTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
* * *
968594 TTTATCTCTCTCAAGATTGTTTTTCCTTAAAACAAAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
968634 TTTATCTC
1 TTTATCTC
968642 GCTTGAGATA
Statistics
Matches: 425, Mismatches: 21, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 0.09
40 388 0.91
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (40 bp):
TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
Found at i:968684 original size:39 final size:40
Alignment explanation
Indices: 968155--968741 Score: 616
Period size: 40 Copynumber: 14.8 Consensus size: 40
968145 ATATAGAGGA
* * * *
968155 TTTATCTCACTGAAGATTGTTTTTCCTTGAAACAGAAGAT
1 TTTATCTCGCTCAAGATAGTTTTCCCTTGAAACAGAAGAT
** * *
968195 TTTATCTCATTCAAGATTGTTTTTCCTTGAAACAGAAGAT
1 TTTATCTCGCTCAAGATAGTTTTCCCTTGAAACAGAAGAT
* ** * * *
968235 TTTATTTCATTCAAGATTGTTTTTCCTCGAAACAGAAGAT
1 TTTATCTCGCTCAAGATAGTTTTCCCTTGAAACAGAAGAT
* ** * * *
968275 TTTATTTCATTCAAGATTGTTTTTCCTTGAAACAAAAGAT
1 TTTATCTCGCTCAAGATAGTTTTCCCTTGAAACAGAAGAT
* * *
968315 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
1 TTTATCTCGCTCAAGATAGTTTTCCCTTGAAACAGAAGAT
* * **
968355 TTTATCTCACTCAAGATTGTTTTTTCTTGAAACAGAAGAT
1 TTTATCTCGCTCAAGATAGTTTTCCCTTGAAACAGAAGAT
* * * *
968395 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACATAAGAT
1 TTTATCTCGCTCAAGATAGTTTTCCCTTGAAACAGAAGAT
968435 TTTATCTCGCTCAAGATTA-TTTT-CCTTGAAACAGAAGAT
1 TTTATCTCGCTCAAGA-TAGTTTTCCCTTGAAACAGAAGAT
* *
968474 TTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAGAAGAT
1 TTTATCTCGCTCAAGATAGTTTTCCCTTGAAACAGAAGAT
*
968514 TTTATCTCGCTCAAGATTGTTTTTCCC-TGAAACAGAAGAT
1 TTTATCTCGCTCAAGATAG-TTTTCCCTTGAAACAGAAGAT
* *
968554 TTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAGAAGAT
1 TTTATCTCGCTCAAGATAGTTTTCCCTTGAAACAGAAGAT
* * * * *
968594 TTTATCTCTCTCAAGATTGTTTTTCCTTAAAACAAAAGAT
1 TTTATCTCGCTCAAGATAGTTTTCCCTTGAAACAGAAGAT
** * * *
968634 TTTATCTCGCTTGAGATAG-TTTCCCTCGAAATAAAAGAT
1 TTTATCTCGCTCAAGATAGTTTTCCCTTGAAACAGAAGAT
** *
968673 TTTATCTCGCTTGAGATAG-TTTCCCTTG-AA-ATAA-AT
1 TTTATCTCGCTCAAGATAGTTTTCCCTTGAAACAGAAGAT
* * **
968709 TTTGTCTCACTTGAGATAG-TTTCCCTTGAAACA
1 TTTATCTCGCTCAAGATAGTTTTCCCTTGAAACA
968742 AGTTTTGTCT
Statistics
Matches: 507, Mismatches: 33, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
36 28 0.06
37 5 0.01
38 4 0.01
39 84 0.17
40 379 0.75
41 7 0.01
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (40 bp):
TTTATCTCGCTCAAGATAGTTTTCCCTTGAAACAGAAGAT
Found at i:968722 original size:36 final size:36
Alignment explanation
Indices: 968632--968775 Score: 180
Period size: 36 Copynumber: 3.9 Consensus size: 36
968622 AAAACAAAAG
*
968632 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAATAAAA
1 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAT--AA
968670 GATTTTATCTCGCTTGAGATAGTTTCCCTTGAAATAA
1 -ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAATAA
* * *
968707 ATTTTGTCTCACTTGAGATAGTTTCCCTTGAAACAA
1 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAATAA
* * * * *
968743 GTTTTGTCTCCCTTGAAATAGTTTCTCTTGAAA
1 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAA
968776 ATTTTGAGAA
Statistics
Matches: 97, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
36 62 0.64
37 2 0.02
39 33 0.34
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (36 bp):
ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAATAA
Found at i:968833 original size:36 final size:36
Alignment explanation
Indices: 968779--968892 Score: 115
Period size: 36 Copynumber: 3.2 Consensus size: 36
968769 CTTGAAAATT
*
968779 TTGAGAACA-TTTCCCTTGAAACGAATTTTGTCTCCC
1 TTGAG-ACAGTTTCTCTTGAAACGAATTTTGTCTCCC
*
968815 TTGAGACAGTTTCTCTTGAAACAGAGTTTTGTCTCCC
1 TTGAGACAGTTTCTCTTGAAAC-GAATTTTGTCTCCC
* * * * * * *
968852 TTAAGA-TGTTTTTCTTAAAACCAAATTTGTCTCAC
1 TTGAGACAGTTTCTCTTGAAACGAATTTTGTCTCCC
968887 TTGAGA
1 TTGAGA
968893 TGGTTTTTCT
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
35 18 0.28
36 29 0.45
37 18 0.28
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (36 bp):
TTGAGACAGTTTCTCTTGAAACGAATTTTGTCTCCC
Found at i:968990 original size:29 final size:28
Alignment explanation
Indices: 968912--968993 Score: 112
Period size: 28 Copynumber: 2.9 Consensus size: 28
968902 TAAAAATCCC
968912 TTGAGACAATTTTCCTTTGAAACAAGTTT
1 TTGAGACAATTTTCC-TTGAAACAAGTTT
* *
968941 TTGAGA-TAGTTTCTCTTGAAACAAGTTT
1 TTGAGACAATTTTC-CTTGAAACAAGTTT
968969 TTGAGACAATTTTCCTTCGAAACAA
1 TTGAGACAATTTTCCTT-GAAACAA
968994 AATTTATCTC
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
28 27 0.59
29 19 0.41
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.39
Consensus pattern (28 bp):
TTGAGACAATTTTCCTTGAAACAAGTTT
Found at i:969045 original size:61 final size:61
Alignment explanation
Indices: 968969--969193 Score: 344
Period size: 61 Copynumber: 3.7 Consensus size: 61
968959 AAACAAGTTT
968969 TTGAGACAATTTTCCTTCGAAACAAAATTTATCTCAATTGAGATGGTTTTTCTTAAAACCC
1 TTGAGACAATTTTCCTTCGAAACAAAATTTATCTCAATTGAGATGGTTTTTCTTAAAACCC
* * * *
969030 TTGAGATAGTTTTCCTTTGAAACAAAATTTATCTCGATTGAGATGGTTTTTCTTAAAACCC
1 TTGAGACAATTTTCCTTCGAAACAAAATTTATCTCAATTGAGATGGTTTTTCTTAAAACCC
** * *
969091 TTGAGACGGTTTTCCTTTGAAACAAAATTTATCTCATTTGAGATGGTTTTTCTTAAAA-CC
1 TTGAGACAATTTTCCTTCGAAACAAAATTTATCTCAATTGAGATGGTTTTTCTTAAAACCC
** *
969151 TTGAGACAATTTTCCTTCGAGGCAAAATTTATCTCACTTGAGA
1 TTGAGACAATTTTCCTTCGAAACAAAATTTATCTCAATTGAGA
969194 GAGCTTCTCT
Statistics
Matches: 150, Mismatches: 14, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
60 39 0.26
61 111 0.74
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (61 bp):
TTGAGACAATTTTCCTTCGAAACAAAATTTATCTCAATTGAGATGGTTTTTCTTAAAACCC
Found at i:969530 original size:20 final size:20
Alignment explanation
Indices: 969467--969530 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
969457 TCCAGTATAG
*
969467 AGTTCATAATGAGAATAACT
1 AGTTCATAATGAGAAGAACT
* * **
969487 CG-TC-TAACGAGGAAGAAGA
1 AGTTCATAATGA-GAAGAACT
969506 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
*
969526 TGTTC
1 AGTTC
969531 GAACTCACAT
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
18 5 0.16
19 8 0.26
20 13 0.42
21 5 0.16
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.25
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:969790 original size:136 final size:135
Alignment explanation
Indices: 969546--969887 Score: 473
Period size: 136 Copynumber: 2.6 Consensus size: 135
969536 CACATTAGTG
* *
969546 TTTCCAATGGAGAGTTCATAATGAGAAGAATTCATCCAATAGAGGGAGAAGAAGTTCATAATGAG
1 TTTCCAAT-GAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTTCATAATGAG
* * *
969611 AAGAGCTTGTTTGACCTATCACTCGATTCACGGCATTTCGAATCAGTGATATCTCGCTT-GAGGG
65 AAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCG-TTAGAGGG
*
969675 ATTGATA
129 ATTGACA
* *
969682 TTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGGGAAGAAGTTCATAATGAG
1 TTTCCAA-TGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTTCATAATGAG
* *
969747 AATAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACGCCTCGTTAGAGGGA
65 AAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCGTTAGAGGGA
969812 TTGACA
130 TTGACA
* * **
969818 TTTCCAA-AAGAGTTCATAATGAGAATAACTCATCTTA-A-A-GGAG-A-AAGTTCATAATGAGA
1 TTTCCAATGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTTCATAATGAGA
*
969877 AGAACTTGTTC
66 AGAGCTTGTTC
969888 CTTTCAAGTC
Statistics
Matches: 187, Mismatches: 17, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
129 24 0.13
130 1 0.01
131 3 0.02
132 1 0.01
133 1 0.01
134 26 0.14
135 2 0.01
136 128 0.68
137 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (135 bp):
TTTCCAATGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTTCATAATGAGA
AGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCGTTAGAGGGAT
TGACA
Found at i:970261 original size:3 final size:3
Alignment explanation
Indices: 970255--970288 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
970245 CAAAAAAATA
*
970255 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
970289 ATACAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 1 0.04
3 27 0.96
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:971781 original size:12 final size:12
Alignment explanation
Indices: 971764--971789 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
971754 CTCAGATTAA
971764 TTTTTTTTAATT
1 TTTTTTTTAATT
971776 TTTTTTTTAATT
1 TTTTTTTTAATT
971788 TT
1 TT
971790 ACCTTTACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTTTAATT
Found at i:972035 original size:2 final size:2
Alignment explanation
Indices: 972028--972056 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
972018 GTGTTTAACT
972028 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
972057 TCTATATTAC
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:972132 original size:2 final size:2
Alignment explanation
Indices: 972125--972179 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
972115 TCATAAGTAT
972125 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
972167 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
972180 TGAATATGCT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:972344 original size:23 final size:23
Alignment explanation
Indices: 972318--972375 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
972308 ATATGTGATC
**
972318 GTATGACATTTTTTACATAAATT
1 GTATGACATCCTTTACATAAATT
*
972341 GTATGACGTCCTTTACATAAATT
1 GTATGACATCCTTTACATAAATT
972364 GTATGACATCCT
1 GTATGACATCCT
972376 CATGTGCATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (23 bp):
GTATGACATCCTTTACATAAATT
Found at i:974112 original size:3 final size:3
Alignment explanation
Indices: 974104--974131 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
974094 CAGTGAACTT
974104 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
974132 GCAAAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:977132 original size:28 final size:27
Alignment explanation
Indices: 977083--977141 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
977073 ATTCCAAAAA
* *
977083 AAAAAACCTTAAATTTCAAAAAATATC
1 AAAAAACCCTAAATTCCAAAAAATATC
* * *
977110 AAAAAACTCCTAAATTCCTAAAATTCTC
1 AAAAAAC-CCTAAATTCCAAAAAATATC
977138 AAAA
1 AAAA
977142 CCCATAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 7 0.27
28 19 0.73
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.25
Consensus pattern (27 bp):
AAAAAACCCTAAATTCCAAAAAATATC
Found at i:987470 original size:27 final size:25
Alignment explanation
Indices: 987415--987472 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 25
987405 GGTATTTTAT
*
987415 AATTTTAGGTTTTTTTTAAATACAT
1 AATTTTAGGTTTTTTTTAAATACAA
*
987440 AATTTTAAGTTTTATTTTTAAAATA-AA
1 AATTTT-AGGTTT-TTTTT-AAATACAA
987467 AATTTT
1 AATTTT
987473 CAAAAAGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 6 0.21
26 5 0.18
27 12 0.43
28 5 0.18
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (25 bp):
AATTTTAGGTTTTTTTTAAATACAA
Found at i:998446 original size:17 final size:17
Alignment explanation
Indices: 998421--998459 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
998411 CAATTTGAAC
*
998421 TTGAATTTTTTTTCGAG
1 TTGAGTTTTTTTTCGAG
998438 TTGAG-TTTTTTTCGAG
1 TTGAGTTTTTTTTCGAG
998454 TTGAGT
1 TTGAGT
998460 CGAGATTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.15, C:0.05, G:0.23, T:0.56
Consensus pattern (17 bp):
TTGAGTTTTTTTTCGAG
Found at i:998448 original size:16 final size:16
Alignment explanation
Indices: 998427--998459 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
998417 GAACTTGAAT
998427 TTTTTTTCGAGTTGAG
1 TTTTTTTCGAGTTGAG
998443 TTTTTTTCGAGTTGAG
1 TTTTTTTCGAGTTGAG
998459 T
1 T
998460 CGAGATTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.06, G:0.24, T:0.58
Consensus pattern (16 bp):
TTTTTTTCGAGTTGAG
Found at i:1001712 original size:3 final size:3
Alignment explanation
Indices: 1001704--1001734 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1001694 GGTTCATTAG
1001704 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1001735 ACCTGATGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:1005826 original size:14 final size:15
Alignment explanation
Indices: 1005809--1005845 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
1005799 AATATTACAA
1005809 TAAAATTATAAT-TT
1 TAAAATTATAATATT
1005823 TAAAATTATAATAATT
1 TAAAATTATAAT-ATT
1005839 TAAAATT
1 TAAAATT
1005846 TTCAAAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 12 0.57
16 9 0.43
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TAAAATTATAATATT
Found at i:1005986 original size:20 final size:20
Alignment explanation
Indices: 1005961--1006010 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1005951 CTGTTTGTTT
*
1005961 GGCTCTGAATAGAATAATTC
1 GGCTCTGAATAGAAGAATTC
*
1005981 GGCTCTGAATGGAAGAATTC
1 GGCTCTGAATAGAAGAATTC
* *
1006001 AGCGCTGAAT
1 GGCTCTGAAT
1006011 GCTGAATCGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (20 bp):
GGCTCTGAATAGAAGAATTC
Found at i:1010049 original size:3 final size:3
Alignment explanation
Indices: 1010043--1010191 Score: 207
Period size: 3 Copynumber: 51.0 Consensus size: 3
1010033 TTTTTATCCA
* ** *
1010043 TAT TAT TAT TAT TAA TAT TAT TAT TAT CCT TAT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
1010091 TAT TAT TAT TAT TAT TAT TA- TAT TAC TAT TAT CAT TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1010137 TAT TAT TA- TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1010183 TAT TAT TAT
1 TAT TAT TAT
1010192 ATAAAATATA
Statistics
Matches: 128, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
2 8 0.06
3 120 0.94
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1010208 original size:10 final size:9
Alignment explanation
Indices: 1010189--1010247 Score: 52
Period size: 9 Copynumber: 6.8 Consensus size: 9
1010179 TTATTATTAT
1010189 TATATAAAA
1 TATATAAAA
*
1010198 TATATTAAA
1 TATATAAAA
1010207 -ATATAAAA
1 TATATAAAA
* *
1010215 TAAATAATA
1 TATATAAAA
1010224 TA-ATAAAA
1 TATATAAAA
*
1010232 AATAATAAAA
1 TAT-ATAAAA
1010242 -ATATAA
1 TATATAA
1010248 TTACAGGCCC
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
8 17 0.41
9 18 0.44
10 6 0.15
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
TATATAAAA
Found at i:1010228 original size:19 final size:16
Alignment explanation
Indices: 1010190--1010247 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 16
1010180 TATTATTATT
*
1010190 ATATAAAATATATTAAA
1 ATATAAAATA-ATAAAA
1010207 ATATAAAATAAATAATATA
1 ATATAAAAT-AATAA-A-A
*
1010226 ATAAAAAATAATAAAA
1 ATATAAAATAATAAAA
1010242 ATATAA
1 ATATAA
1010248 TTACAGGCCC
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
16 6 0.17
17 13 0.37
18 7 0.20
19 9 0.26
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
ATATAAAATAATAAAA
Found at i:1010230 original size:24 final size:21
Alignment explanation
Indices: 1010194--1010248 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 21
1010184 ATTATTATAT
*
1010194 AAAATATATTAAAATATAAAATA
1 AAAATATAATAAAA-A-AAAATA
*
1010217 AATAATATAATAAAAAATAATA
1 AA-AATATAATAAAAAAAAATA
1010239 AAAATATAAT
1 AAAATATAAT
1010249 TACAGGCCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 8 0.28
22 7 0.24
23 3 0.10
24 11 0.38
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAATATAATAAAAAAAAATA
Found at i:1010731 original size:18 final size:19
Alignment explanation
Indices: 1010708--1010745 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1010698 AGAGACAGAG
1010708 ACAGAG-AAGAAAAAAAAA
1 ACAGAGAAAGAAAAAAAAA
1010726 ACAGAGAAAGAAAAAAAAA
1 ACAGAGAAAGAAAAAAAAA
1010745 A
1 A
1010746 AATATACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.79, C:0.05, G:0.16, T:0.00
Consensus pattern (19 bp):
ACAGAGAAAGAAAAAAAAA
Found at i:1011869 original size:17 final size:18
Alignment explanation
Indices: 1011844--1011896 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 18
1011834 AGATATTTTT
1011844 AAATAAATATAATTTTGA
1 AAATAAATATAATTTTGA
* *
1011862 AAAT-AATAGAATTAT-A
1 AAATAAATATAATTTTGA
* *
1011878 AATTAAATATATTTTTGA
1 AAATAAATATAATTTTGA
1011896 A
1 A
1011897 TTTTTTAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
16 4 0.15
17 17 0.63
18 6 0.22
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.40
Consensus pattern (18 bp):
AAATAAATATAATTTTGA
Found at i:1022983 original size:11 final size:11
Alignment explanation
Indices: 1022967--1023014 Score: 78
Period size: 11 Copynumber: 4.2 Consensus size: 11
1022957 ATTATGCTTG
1022967 AAGAAAAAAAA
1 AAGAAAAAAAA
1022978 AAGAAAAAAAA
1 AAGAAAAAAAA
1022989 AAGAAAAAAAA
1 AAGAAAAAAAA
1023000 AAGGAAAAAAGAA
1 AA-GAAAAAA-AA
1023013 AA
1 AA
1023015 AGGGGGTCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
11 24 0.69
12 7 0.20
13 4 0.11
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:1022987 original size:12 final size:12
Alignment explanation
Indices: 1022970--1023016 Score: 69
Period size: 12 Copynumber: 3.9 Consensus size: 12
1022960 ATGCTTGAAG
1022970 AAAAAAAAAAG-
1 AAAAAAAAAAGA
1022981 AAAAAAAAAAGA
1 AAAAAAAAAAGA
*
1022993 AAAAAAAAAGGA
1 AAAAAAAAAAGA
1023005 AAAAAGAAAAAG
1 AAAAA-AAAAAG
1023017 GGGGTCAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 11 0.34
12 16 0.50
13 5 0.16
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:1023379 original size:19 final size:20
Alignment explanation
Indices: 1023346--1023387 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
1023336 TTCAAGTTCA
*
1023346 ATTTATTGGAGATTCAATTT
1 ATTTATTGGAAATTCAATTT
1023366 ATTT-TTGGAAATTCAATTT
1 ATTTATTGGAAATTCAATTT
1023385 ATT
1 ATT
1023388 CTTTTCTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (20 bp):
ATTTATTGGAAATTCAATTT
Found at i:1024299 original size:52 final size:52
Alignment explanation
Indices: 1024171--1024639 Score: 847
Period size: 52 Copynumber: 9.1 Consensus size: 52
1024161 ATTTGCCAAT
* *
1024171 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAT--
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCA
1024221 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCA
* * * *
1024273 AGCATCTTCTAGAAGTGTTATTTGAGTTATCTGATCTGGTTAGACAGAAT--
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCA
1024323 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCA
1024375 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCA
1024427 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCA
1024479 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCA
1024531 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCA
*
1024583 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCA
1024635 AGCAT
1 AGCAT
1024640 TGAATTTAGA
Statistics
Matches: 404, Mismatches: 11, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
50 94 0.23
52 310 0.77
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (52 bp):
AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCA
Found at i:1024722 original size:83 final size:83
Alignment explanation
Indices: 1024583--1024826 Score: 409
Period size: 83 Copynumber: 3.0 Consensus size: 83
1024573 GACAGAATCA
*
1024583 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAAGCATTGAATTTA
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAAGCATTGAATTTG
1024648 GAAGATGAATTTGCCAAT
66 GAAGATGAATTTGCCAAT
* * ** *
1024666 AGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGATTATATAGAATCAAGCATTGAATTTG
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAAGCATTGAATTTG
1024731 GAAGATGAATTTGCCAAT
66 GAAGATGAATTTGCCAAT
* *
1024749 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTTGGACAGAA-CAATCATTGAATTTG
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAAGCATTGAATTTG
1024813 GAAGATGAATTTGC
66 GAAGATGAATTTGC
1024827 TCATAGTAAA
Statistics
Matches: 148, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
82 28 0.19
83 120 0.81
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.37
Consensus pattern (83 bp):
AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAATCAAGCATTGAATTTG
GAAGATGAATTTGCCAAT
Found at i:1025638 original size:113 final size:113
Alignment explanation
Indices: 1025440--1025871 Score: 706
Period size: 113 Copynumber: 3.8 Consensus size: 113
1025430 CAAAGATTCA
*
1025440 AATCCATCATTTGATGGAGCAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGAGCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1025505 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
*
1025553 AATCCATCATTTGATGGAGCAGCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGAGCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1025618 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * *
1025666 AATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGAGCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * *
1025731 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
66 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * * * * *
1025779 AATTCATCATTTAATGGATCAACATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCATTTGATGGAGCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAG
1025843 AAGGAAGAA-AAAGTTCATAATGAGAAGAA
65 AAGGAAGAAGAAA-TTCATAATGAGAAGAA
1025872 CTCATCAAGA
Statistics
Matches: 303, Mismatches: 14, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
112 3 0.01
113 300 0.99
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.27
Consensus pattern (113 bp):
AATCCATCATTTGATGGAGCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
Found at i:1026130 original size:3 final size:3
Alignment explanation
Indices: 1026124--1026275 Score: 250
Period size: 3 Copynumber: 50.7 Consensus size: 3
1026114 TTTTTATCCA
** *
1026124 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CCT TAT TAT TAT TAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
1026172 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1026220 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1026268 TAT TAT TA
1 TAT TAT TA
1026276 AATATATTAA
Statistics
Matches: 137, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 137 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1026315 original size:20 final size:19
Alignment explanation
Indices: 1026274--1026318 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1026264 CTATTATTAT
* *
1026274 TAAATATATTAAATACATA
1 TAAATATATTAAAAACAAA
*
1026293 TAAATATTATTAAAAATAAA
1 TAAATA-TATTAAAAACAAA
1026313 TAAATA
1 TAAATA
1026319 ATAAAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAATATATTAAAAACAAA
Found at i:1026817 original size:23 final size:21
Alignment explanation
Indices: 1026791--1026833 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1026781 GAAACTAGAG
*
1026791 ACAGAGACAGAGAAGAAAAAAAA
1 ACAGAGA-AAAGAA-AAAAAAAA
1026814 ACAGAGAAAAGAAAAAAAAA
1 ACAGAGAAAAGAAAAAAAAA
1026834 CAAATATACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 5 0.26
23 7 0.37
ACGTcount: A:0.74, C:0.07, G:0.19, T:0.00
Consensus pattern (21 bp):
ACAGAGAAAAGAAAAAAAAAA
Found at i:1026819 original size:17 final size:18
Alignment explanation
Indices: 1026797--1026835 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
1026787 AGAGACAGAG
1026797 ACAGAG-AAGAAAAAAAA
1 ACAGAGAAAGAAAAAAAA
1026814 ACAGAGAAAAGAAAAAAAA
1 ACAGAG-AAAGAAAAAAAA
1026833 ACA
1 ACA
1026836 AATATACCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.30
19 14 0.70
ACGTcount: A:0.77, C:0.08, G:0.15, T:0.00
Consensus pattern (18 bp):
ACAGAGAAAGAAAAAAAA
Found at i:1027973 original size:17 final size:18
Alignment explanation
Indices: 1027948--1028000 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 18
1027938 AGATATTTTT
1027948 AAATAAATATAATTTTGA
1 AAATAAATATAATTTTGA
* *
1027966 AAAT-AATAGAATTAT-A
1 AAATAAATATAATTTTGA
* *
1027982 AATTAAATATATTTTTGA
1 AAATAAATATAATTTTGA
1028000 A
1 A
1028001 TTTTTTAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
16 4 0.15
17 17 0.63
18 6 0.22
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.40
Consensus pattern (18 bp):
AAATAAATATAATTTTGA
Found at i:1028808 original size:21 final size:22
Alignment explanation
Indices: 1028784--1028832 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
1028774 TTTTAAAATG
1028784 ATTTATATATT-TTTATTTAAA
1 ATTTATATATTATTTATTTAAA
* *
1028805 ATTTAT-TTTTATTTTTTTAAA
1 ATTTATATATTATTTATTTAAA
*
1028826 TTTTATA
1 ATTTATA
1028833 AGTTCACTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
ATTTATATATTATTTATTTAAA
Found at i:1029324 original size:16 final size:16
Alignment explanation
Indices: 1029303--1029356 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
1029293 CCCGATTATA
1029303 TATATTTTTTATATTT
1 TATATTTTTTATATTT
*
1029319 TATATTTTTTATATAT
1 TATATTTTTTATATTT
* *
1029335 AATATTTTATATATTT
1 TATATTTTTTATATTT
1029351 TATATT
1 TATATT
1029357 AATTATATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TATATTTTTTATATTT
Found at i:1029343 original size:23 final size:22
Alignment explanation
Indices: 1029298--1029359 Score: 76
Period size: 23 Copynumber: 2.9 Consensus size: 22
1029288 CCCGCCCCGA
1029298 TTATATATATTT-T-TT-ATATT
1 TTATATAT-TTTATATTAATATT
*
1029318 TTATATTTTTTATATATAATATT
1 TTATATATTTTATAT-TAATATT
1029341 TTATATATTTTATATTAAT
1 TTATATATTTTATATTAAT
1029360 TATATATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
19 3 0.08
20 8 0.22
21 1 0.03
22 5 0.14
23 19 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TTATATATTTTATATTAATATT
Found at i:1029348 original size:32 final size:32
Alignment explanation
Indices: 1029299--1029368 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
1029289 CCGCCCCGAT
* **
1029299 TATAT-ATATTTTTTATATTTTATATTTTTTA
1 TATATAATATTTTATATATTTTATATTAATTA
1029330 TATATAATATTTTATATATTTTATATTAATTA
1 TATATAATATTTTATATATTTTATATTAATTA
1029362 TATATAA
1 TATATAA
1029369 AATATTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
31 5 0.14
32 30 0.86
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (32 bp):
TATATAATATTTTATATATTTTATATTAATTA
Found at i:1031540 original size:3 final size:3
Alignment explanation
Indices: 1031532--1031565 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1031522 AAAAGACTTC
1031532 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1031566 TCTTTCATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1039541 original size:38 final size:38
Alignment explanation
Indices: 1039497--1039615 Score: 238
Period size: 38 Copynumber: 3.1 Consensus size: 38
1039487 TAGTTAATTT
1039497 TATGTTGATGAATTTTACTTTCTTTTCTAAGTATACAA
1 TATGTTGATGAATTTTACTTTCTTTTCTAAGTATACAA
1039535 TATGTTGATGAATTTTACTTTCTTTTCTAAGTATACAA
1 TATGTTGATGAATTTTACTTTCTTTTCTAAGTATACAA
1039573 TATGTTGATGAATTTTACTTTCTTTTCTAAGTATACAA
1 TATGTTGATGAATTTTACTTTCTTTTCTAAGTATACAA
1039611 TATGT
1 TATGT
1039616 ATATGCTTTT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 81 1.00
ACGTcount: A:0.29, C:0.10, G:0.11, T:0.50
Consensus pattern (38 bp):
TATGTTGATGAATTTTACTTTCTTTTCTAAGTATACAA
Found at i:1044622 original size:19 final size:20
Alignment explanation
Indices: 1044590--1044627 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1044580 TTACATGATT
* *
1044590 ATAATTTAAGAAAT-ATTTC
1 ATAATTAAAAAAATGATTTC
1044609 ATAATTAAAAAAATGATTT
1 ATAATTAAAAAAATGATTT
1044628 TTCATATACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (20 bp):
ATAATTAAAAAAATGATTTC
Found at i:1048690 original size:31 final size:31
Alignment explanation
Indices: 1048652--1048715 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
1048642 TATCGATCTA
1048652 ATCCAAAAATGATATAACTTCTAATTCAGAT
1 ATCCAAAAATGATATAACTTCTAATTCAGAT
*
1048683 ATCCAAAAATGATATAACTTCTAATTCATAT
1 ATCCAAAAATGATATAACTTCTAATTCAGAT
1048714 AT
1 AT
1048716 GTCAATAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.34
Consensus pattern (31 bp):
ATCCAAAAATGATATAACTTCTAATTCAGAT
Found at i:1056515 original size:445 final size:445
Alignment explanation
Indices: 1055686--1056575 Score: 1717
Period size: 445 Copynumber: 2.0 Consensus size: 445
1055676 AACTTAGAAG
1055686 AAATCATGTTGTAGAAGATGACAACAATCAGGAGAAATTTGCAGCAAGGATAGCAATTATTTTGA
1 AAATCATGTTGTAGAAGATGACAACAATCAGGAGAAATTTGCAGCAAGGATAGCAATTATTTTGA
*
1055751 ACCCCAAGGGAAATGAAAGGTTCAATGAAGATTTTTGCACCAAGTTCTTGTTAAAATCTAACTGA
66 ACCCCAAGGGAAATGAAAGGTTCAATGAAGATTTTTGCACCAAGTTCTTGTTAAAATCTAACAGA
*
1055816 GATTTGAGAGATCTCATTTTCATAAAACCATTGCACGTGAGCATAAAGTTCAATTCTCATAATCA
131 GATTTGAGAGATCTCATTTTCATAAAACCATTGCACGTGAGAATAAAGTTCAATTCTCATAATCA
1055881 CCCAAAAGCTGAAAACTCAAAAGACATCATCTTAACTGACTCCTCCATTAAAGTTGATGTGTCCT
196 CCCAAAAGCTGAAAACTCAAAAGACATCATCTTAACTGACTCCTCCATTAAAGTTGATGTGTCCT
1055946 TGAACCGAAGGCATGATGTTGATGCTGCCATATTTTTATAATTCAACCCTGCTGTATTGATGTAC
261 TGAACCGAAGGCATGATGTTGATGCTGCCATATTTTTATAATTCAACCCTGCTGTATTGATGTAC
*
1056011 CATGAAGGTTTTTTCTTTTTCGTTGATCTTATTCTGTGATTTCCTACTGGAACTTTGTATAGTTA
326 CATGAAGGTTTTTTCTTTTTCGTTGATCTTATTCTGGGATTTCCTACTGGAACTTTGTATAGTTA
* *
1056076 ATTTTTTACTACAATTCAGATTTTTAACAATGGGCTTAAATTACTCGATGGGCTT
391 ATTTTTTACTACAATTCAGATTTTTAACAATGGGCTTAAATTACTAGATAGGCTT
1056131 AAATCATGTTGTAGAAGATGACAACAATCAGGAGAAATTTGCAGCAAGGATAGCAATTATTTTGA
1 AAATCATGTTGTAGAAGATGACAACAATCAGGAGAAATTTGCAGCAAGGATAGCAATTATTTTGA
1056196 ACCCCAAGGGAAATGAAAGGTTCAATGAAGATTTTTGCACCAAGTTCTTGTTAAAATCTAACAGA
66 ACCCCAAGGGAAATGAAAGGTTCAATGAAGATTTTTGCACCAAGTTCTTGTTAAAATCTAACAGA
*
1056261 GATTTGAGAGATCTCATTTTCATAAACCCATTGCACGTGAGAATAAAGTTCAATTCTCATAATCA
131 GATTTGAGAGATCTCATTTTCATAAAACCATTGCACGTGAGAATAAAGTTCAATTCTCATAATCA
1056326 CCCAAAAGCTGAAAACTCAAAAGACATCATCTTAACTGACTCCTCCATTAAAGTTGATGTGTCCT
196 CCCAAAAGCTGAAAACTCAAAAGACATCATCTTAACTGACTCCTCCATTAAAGTTGATGTGTCCT
*
1056391 TGAACCGAAGGCATGATGTTGATGCTGCCATATTTTTATAATTCAACCCTGCTGTATTGATTTAC
261 TGAACCGAAGGCATGATGTTGATGCTGCCATATTTTTATAATTCAACCCTGCTGTATTGATGTAC
1056456 CATGAAGGTTTTTTCTTTTTCGTTGATCTTATTCTGGGATTTCCTACTGGAACTTTGTATAGTTA
326 CATGAAGGTTTTTTCTTTTTCGTTGATCTTATTCTGGGATTTCCTACTGGAACTTTGTATAGTTA
1056521 ATTTTTTACTACAATTCAGATTTTTAACAATGGGCTTAAATTACTAGATAGGCTT
391 ATTTTTTACTACAATTCAGATTTTTAACAATGGGCTTAAATTACTAGATAGGCTT
1056576 CTTCACTCTA
Statistics
Matches: 438, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
445 438 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (445 bp):
AAATCATGTTGTAGAAGATGACAACAATCAGGAGAAATTTGCAGCAAGGATAGCAATTATTTTGA
ACCCCAAGGGAAATGAAAGGTTCAATGAAGATTTTTGCACCAAGTTCTTGTTAAAATCTAACAGA
GATTTGAGAGATCTCATTTTCATAAAACCATTGCACGTGAGAATAAAGTTCAATTCTCATAATCA
CCCAAAAGCTGAAAACTCAAAAGACATCATCTTAACTGACTCCTCCATTAAAGTTGATGTGTCCT
TGAACCGAAGGCATGATGTTGATGCTGCCATATTTTTATAATTCAACCCTGCTGTATTGATGTAC
CATGAAGGTTTTTTCTTTTTCGTTGATCTTATTCTGGGATTTCCTACTGGAACTTTGTATAGTTA
ATTTTTTACTACAATTCAGATTTTTAACAATGGGCTTAAATTACTAGATAGGCTT
Found at i:1059136 original size:4 final size:4
Alignment explanation
Indices: 1059127--1059227 Score: 64
Period size: 4 Copynumber: 25.0 Consensus size: 4
1059117 GACAATATAC
* * * * *
1059127 ATAA ATAA ATGA ATAA ATAA ATAA ACAA ATATGA GTAA ATAA ATCA A-AG
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA--A ATAA ATAA ATAA ATAA
* * * *
1059176 ATAA AGAA A-AA A-AA GAAAA ATAA ATAA ATAG ATAA CTAA ATAA ATAA
1 ATAA ATAA ATAA ATAA -ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1059223 GATAA
1 -ATAA
1059228 GGAAAAAATA
Statistics
Matches: 75, Mismatches: 16, Indels: 11
0.74 0.16 0.11
Matches are distributed among these distances:
3 6 0.08
4 60 0.80
5 6 0.08
6 3 0.04
ACGTcount: A:0.69, C:0.03, G:0.08, T:0.20
Consensus pattern (4 bp):
ATAA
Found at i:1059236 original size:16 final size:17
Alignment explanation
Indices: 1059163--1059238 Score: 61
Period size: 16 Copynumber: 4.6 Consensus size: 17
1059153 AAATATGAGT
1059163 AAATAAATCAAAGATAAAG
1 AAATAAAT--AAGATAAAG
* *
1059182 AAA-AAA-AAGAAAAAT
1 AAATAAATAAGATAAAG
**
1059197 AAATAAAT-AGATAACT
1 AAATAAATAAGATAAAG
*
1059213 AAATAAATAAGATAAGG
1 AAATAAATAAGATAAAG
1059230 AAA-AAATAA
1 AAATAAATAA
1059239 TATGTACATA
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
15 10 0.21
16 23 0.48
17 9 0.19
18 3 0.06
19 3 0.06
ACGTcount: A:0.72, C:0.03, G:0.09, T:0.16
Consensus pattern (17 bp):
AAATAAATAAGATAAAG
Found at i:1059498 original size:2 final size:2
Alignment explanation
Indices: 1059491--1059515 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1059481 ACAATAAAAG
1059491 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 T
1059516 GTACATATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1059636 original size:2 final size:2
Alignment explanation
Indices: 1059629--1059676 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1059619 ATAAAATACG
*
1059629 AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1059671 AT AT AT
1 AT AT AT
1059677 TAGAAAATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1061473 original size:105 final size:105
Alignment explanation
Indices: 1061267--1062037 Score: 1176
Period size: 105 Copynumber: 7.4 Consensus size: 105
1061257 GTATTGTTCC
* * * * * * * * *
1061267 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGTTTTGGAACTGGGAAATTATATATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGT-TGTTGACAA
*
1061332 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1061373 GAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTTGTTGACAAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAC
*
1061438 CAGCGGTCCCTTCTTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1061478 GAGTCCAATATCTTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAC
*
1061543 TAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1061583 GAGTCCAATATCCCTCGCTGTG-A---G--ATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAC
*
1061642 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1061682 GAGACCAATATACTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAA
*
1061747 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1061788 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGTTCTGAAATTGGGAAGTTGTTGTTGACAAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAC
* * * *
1061853 CAGTGGTCCCTTCGTTGTGAAGTTGAACTTGCATTGTCTT
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1061893 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAC
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAC
* *
1061958 CAGCGGTCCCTCCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1061998 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTG
1062038 GCTAAAACTT
Statistics
Matches: 610, Mismatches: 48, Indels: 15
0.91 0.07 0.02
Matches are distributed among these distances:
99 91 0.15
100 1 0.00
101 1 0.00
103 1 0.00
104 1 0.00
105 370 0.61
106 145 0.24
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1072231 original size:10 final size:10
Alignment explanation
Indices: 1072216--1072248 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1072206 GGTAAACAGT
1072216 TAAATAAAAA
1 TAAATAAAAA
1072226 TAAATAAAAA
1 TAAATAAAAA
*
1072236 T-AATAATAA
1 TAAATAAAAA
1072245 TAAA
1 TAAA
1072249 AATAAATGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
TAAATAAAAA
Found at i:1073354 original size:17 final size:16
Alignment explanation
Indices: 1073289--1073356 Score: 50
Period size: 17 Copynumber: 4.1 Consensus size: 16
1073279 AAATAAATCA
*
1073289 AAGATAAAGAAAAAAAA
1 AAGAT-AAGAAAAAAAT
*
1073306 AAGA-AAAAAAATAAAT
1 AAGATAAGAAAA-AAAT
* *
1073322 -AGATAACTAAATAAAT
1 AAGATAA-GAAAAAAAT
1073338 AAGATAAGGAAAAAAAT
1 AAGATAA-GAAAAAAAT
1073355 AA
1 AA
1073357 TATGTACATA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
15 9 0.22
16 9 0.22
17 22 0.55
ACGTcount: A:0.75, C:0.01, G:0.10, T:0.13
Consensus pattern (16 bp):
AAGATAAGAAAAAAAT
Found at i:1081159 original size:24 final size:24
Alignment explanation
Indices: 1081142--1081253 Score: 172
Period size: 24 Copynumber: 4.7 Consensus size: 24
1081132 ATCAAAACAT
*
1081142 AATCCAGGTCAAGTATCAGATCAG
1 AATCCAGGTCAAGTATCAGATCAA
*
1081166 AATCCAGGTCAAGTATTC-GATCAG
1 AATCCAGGTCAAGTA-TCAGATCAA
*
1081190 AATCCAGGTCAAGTATCCGATCAA
1 AATCCAGGTCAAGTATCAGATCAA
*
1081214 AATCCAGGTCAAGTATCCGATCAA
1 AATCCAGGTCAAGTATCAGATCAA
1081238 AATCCAGGTCAAGTAT
1 AATCCAGGTCAAGTAT
1081254 TATAATAGAA
Statistics
Matches: 85, Mismatches: 1, Indels: 4
0.94 0.01 0.04
Matches are distributed among these distances:
23 2 0.02
24 81 0.95
25 2 0.02
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCAGATCAA
Found at i:1083749 original size:13 final size:13
Alignment explanation
Indices: 1083731--1083755 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1083721 AGTTTTGGTC
1083731 AACGGGTCGGGTA
1 AACGGGTCGGGTA
1083744 AACGGGTCGGGT
1 AACGGGTCGGGT
1083756 CGGGTTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.48, T:0.16
Consensus pattern (13 bp):
AACGGGTCGGGTA
Found at i:1090423 original size:3 final size:3
Alignment explanation
Indices: 1090415--1090476 Score: 117
Period size: 3 Copynumber: 21.0 Consensus size: 3
1090405 CATAAAAAAT
1090415 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
1090463 ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA
1090477 TTACACTAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 56 0.97
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1098721 original size:22 final size:22
Alignment explanation
Indices: 1098693--1098739 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
1098683 ATAATTTATT
*
1098693 TTTATT-CCTAACATTTTATAAA
1 TTTATTCCCTAA-ATATTATAAA
1098715 TTTATTCCCTAAATATTATAAA
1 TTTATTCCCTAAATATTATAAA
1098737 TTT
1 TTT
1098740 GTTCTTTAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTATTCCCTAAATATTATAAA
Found at i:1098859 original size:3 final size:3
Alignment explanation
Indices: 1098847--1098893 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
1098837 TTTAGTGTGA
* * * *
1098847 TAT T-T TAT TAT TAT TAT TAT TAT TAG TAG TAG TAG TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1098894 CTGTGTGTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:1103463 original size:13 final size:13
Alignment explanation
Indices: 1103445--1103473 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1103435 CCACCGTACT
1103445 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
1103458 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
1103471 CCG
1 CCG
1103474 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:1104188 original size:3 final size:3
Alignment explanation
Indices: 1104182--1104252 Score: 65
Period size: 3 Copynumber: 24.3 Consensus size: 3
1104172 AATAATTATT
* * *
1104182 TAA TAA TAA T-A TAA TAA TAA T-A TAA TAA TAA TAT TTA TAA TAA CAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** **
1104228 TAA TTT TAA TTT TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
1104253 TTAAGTAAAA
Statistics
Matches: 52, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
2 4 0.08
3 48 0.92
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:1104190 original size:14 final size:11
Alignment explanation
Indices: 1104171--1104215 Score: 72
Period size: 11 Copynumber: 4.1 Consensus size: 11
1104161 TTTGGGTTTG
* *
1104171 TAATAATTATT
1 TAATAATAATA
1104182 TAATAATAATA
1 TAATAATAATA
1104193 TAATAATAATA
1 TAATAATAATA
1104204 TAATAATAATA
1 TAATAATAATA
1104215 T
1 T
1104216 TTATAATAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TAATAATAATA
Done.