Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000426.1 Hibiscus syriacus cultivar Beakdansim tig00000778_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: 3165331
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 15
Found at i:882007 original size:7 final size:7
Alignment explanation
Indices: 881995--882045 Score: 77
Period size: 7 Copynumber: 7.4 Consensus size: 7
881985 GACCCGACCC
881995 GACCGTT
1 GACCGTT
882002 GACCGTT
1 GACCGTT
*
882009 GACCATT
1 GACCGTT
*
882016 GACTGTT
1 GACCGTT
882023 GACCG-T
1 GACCGTT
882029 GACCGTT
1 GACCGTT
882036 GACCGTT
1 GACCGTT
882043 GAC
1 GAC
882046 TTTCTTTGAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
6 6 0.15
7 33 0.85
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.27
Consensus pattern (7 bp):
GACCGTT
Found at i:884295 original size:30 final size:30
Alignment explanation
Indices: 884255--884324 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
884245 AGAATCCCAG
* * *
884255 AGAAAGACAAACACCTATGTCCATATATAC
1 AGAAATACAAACACCTATGACCACATATAC
* * *
884285 AGAAATACAAACGCCTCTGACCACATGTAC
1 AGAAATACAAACACCTATGACCACATATAC
884315 AGAAAATACA
1 AG-AAATACA
884325 GACTATTTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 26 0.79
31 7 0.21
ACGTcount: A:0.47, C:0.24, G:0.11, T:0.17
Consensus pattern (30 bp):
AGAAATACAAACACCTATGACCACATATAC
Found at i:885366 original size:13 final size:13
Alignment explanation
Indices: 885340--885374 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
885330 CAATCCAGGC
885340 GACATACG-GGGT
1 GACATACGAGGGT
885352 GACATACGAGGGT
1 GACATACGAGGGT
885365 GACATACGAG
1 GACATACGAG
885375 CCATATACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 8 0.36
13 14 0.64
ACGTcount: A:0.31, C:0.17, G:0.37, T:0.14
Consensus pattern (13 bp):
GACATACGAGGGT
Found at i:886972 original size:15 final size:15
Alignment explanation
Indices: 886952--886982 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
886942 TATAGAAGTC
886952 TGTTTATGGCTGAAT
1 TGTTTATGGCTGAAT
886967 TGTTTATGGCTGAAT
1 TGTTTATGGCTGAAT
886982 T
1 T
886983 TGAAACTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.26, T:0.48
Consensus pattern (15 bp):
TGTTTATGGCTGAAT
Found at i:887384 original size:17 final size:18
Alignment explanation
Indices: 887362--887408 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
887352 TATGAAATTG
887362 GATTCCAATTCC-TAACA
1 GATTCCAATTCCTTAACA
*
887379 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTAACA
887397 GATTCCAATTCC
1 GATTCCAATTCC
887409 CTCAGAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 12 0.43
18 16 0.57
ACGTcount: A:0.30, C:0.32, G:0.06, T:0.32
Consensus pattern (18 bp):
GATTCCAATTCCTTAACA
Found at i:893305 original size:27 final size:27
Alignment explanation
Indices: 893275--893330 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
893265 TTATTCGGAC
893275 ATGGGTATGTGAACATGTCCGATGTGT
1 ATGGGTATGTGAACATGTCCGATGTGT
893302 ATGGGTATGTGAACATGTCCGATGTGT
1 ATGGGTATGTGAACATGTCCGATGTGT
893329 AT
1 AT
893331 TCGTAATCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.23, C:0.11, G:0.32, T:0.34
Consensus pattern (27 bp):
ATGGGTATGTGAACATGTCCGATGTGT
Found at i:899813 original size:17 final size:17
Alignment explanation
Indices: 899791--899825 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
899781 TTCTTTTATG
*
899791 ATTAATTGATTAATTTT
1 ATTAATTAATTAATTTT
899808 ATTAATTAATTAATTTT
1 ATTAATTAATTAATTTT
899825 A
1 A
899826 GGAAGACGAG
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:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
ATTAATTAATTAATTTT
Found at i:903129 original size:32 final size:32
Alignment explanation
Indices: 903071--903132 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
903061 CCAGGTGAAG
*
903071 CCTTTGACGCTGGGATTGCACAGCGTCTTATC
1 CCTTTGACGCTGGGACTGCACAGCGTCTTATC
**
903103 CCTTTGACGC-GAGGACTGCATGGCGTCTTA
1 CCTTTGACGCTG-GGACTGCACAGCGTCTTA
903133 GCCATGAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 1 0.04
32 25 0.96
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.29
Consensus pattern (32 bp):
CCTTTGACGCTGGGACTGCACAGCGTCTTATC
Found at i:905570 original size:60 final size:61
Alignment explanation
Indices: 905445--905597 Score: 163
Period size: 60 Copynumber: 2.5 Consensus size: 61
905435 TTTCAATTAT
* * **
905445 AAACTTTTGAATATTCTAATTTTCAT-CCTCAAACTATGACTCTTATTCTAAATTAGTCATT
1 AAACTTTTGAATATTCTAA-TTTCATCCCTCAAACTATAACCCTTATTCTAAATTAGTCACC
* * * *
905506 AAACTTTTGAACATTCTAATTTCATCCCT-AAACTATAACCCTCT-TTCTTAATTGGTCCCC
1 AAACTTTTGAATATTCTAATTTCATCCCTCAAACTATAACCCT-TATTCTAAATTAGTCACC
*
905566 AAACTTTTGGATATT-TCAATTTCATCCC-CAAA
1 AAACTTTTGAATATTCT-AATTTCATCCCTCAAA
905598 TCCATGCAAA
Statistics
Matches: 78, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
59 1 0.01
60 55 0.71
61 22 0.28
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41
Consensus pattern (61 bp):
AAACTTTTGAATATTCTAATTTCATCCCTCAAACTATAACCCTTATTCTAAATTAGTCACC
Found at i:905831 original size:60 final size:61
Alignment explanation
Indices: 905720--905862 Score: 166
Period size: 60 Copynumber: 2.4 Consensus size: 61
905710 GAATATACGT
* * * * * *
905720 ATAGTTT-GTGATGAAATTGGAATGTTCAAAAATTTTGGGGACCAATTTAGAACAAAT-GCC
1 ATAGTTTGGGGATAAAATTGAAATGTTCAAAAAGTCTGAGGACCAATTTAGAA-AAATAGCC
* ** *
905780 ATAGTTTGGGGATAAAATTGAAATGTTC-AAAAGTCTGAGGACTAATTTAGAATGATAGTC
1 ATAGTTTGGGGATAAAATTGAAATGTTCAAAAAGTCTGAGGACCAATTTAGAAAAATAGCC
905840 ATAGTTTGGGGATAAAATTGAAA
1 ATAGTTTGGGGATAAAATTGAAA
905863 CATTTAATGT
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
59 2 0.03
60 52 0.73
61 17 0.24
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.31
Consensus pattern (61 bp):
ATAGTTTGGGGATAAAATTGAAATGTTCAAAAAGTCTGAGGACCAATTTAGAAAAATAGCC
Found at i:909448 original size:2 final size:2
Alignment explanation
Indices: 909441--909478 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
909431 TAGTTCCGTT
* *
909441 GA GA GA GA GG GA GG GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
909479 TGTGACCATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (2 bp):
GA
Found at i:921750 original size:2 final size:2
Alignment explanation
Indices: 921745--921784 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
921735 CCATGAATCA
921745 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
921785 GACCTGACTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:923193 original size:32 final size:32
Alignment explanation
Indices: 923157--923218 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
923147 TCTCACCTGC
923157 TATTCAATGGCATATGTTGCATGCTATTAGGT
1 TATTCAATGGCATATGTTGCATGCTATTAGGT
923189 TATTCAATGGCATATGTTGCATGCTATTAG
1 TATTCAATGGCATATGTTGCATGCTATTAG
923219 CTTAAGCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (32 bp):
TATTCAATGGCATATGTTGCATGCTATTAGGT
Found at i:923353 original size:2 final size:2
Alignment explanation
Indices: 923346--923387 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
923336 ATTTTAAAAC
923346 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
923388 TAATTCAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:924640 original size:11 final size:11
Alignment explanation
Indices: 924624--924651 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
924614 ATTTATATAT
924624 ATATTTAAAAA
1 ATATTTAAAAA
924635 ATATTTAAAAA
1 ATATTTAAAAA
924646 ATATTT
1 ATATTT
924652 TTTAAAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
ATATTTAAAAA
Found at i:937448 original size:2 final size:2
Alignment explanation
Indices: 937441--937479 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
937431 ATTAAATAAC
937441 TA 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 TA T
937480 TGTTGGTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:938912 original size:31 final size:31
Alignment explanation
Indices: 938872--938933 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
938862 TGAGAGACTG
* * *
938872 AAATTGAACGGATTGATAATGTTAGGGACCA
1 AAATAGAACGGATCGATAACGTTAGGGACCA
938903 AAATAGAACGGATCGATAACGTTAGGGACCA
1 AAATAGAACGGATCGATAACGTTAGGGACCA
938934 TTCCCCCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.40, C:0.13, G:0.26, T:0.21
Consensus pattern (31 bp):
AAATAGAACGGATCGATAACGTTAGGGACCA
Found at i:944820 original size:2 final size:2
Alignment explanation
Indices: 944815--944846 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
944805 GAAATGTTAA
944815 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
944847 TGTTTTGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:947109 original size:36 final size:35
Alignment explanation
Indices: 947053--947132 Score: 117
Period size: 36 Copynumber: 2.3 Consensus size: 35
947043 ACCCATTCCT
*
947053 ATTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 ATTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
* *
947087 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACC
1 A-TTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
947123 ATTTTCAAAG
1 ATTTTCAAAG
947133 TTGGTTGCCA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
34 1 0.02
35 14 0.34
36 26 0.63
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (35 bp):
ATTTTCAAAGAAACATCTACCAAACTTTGAAAAAC
Found at i:955177 original size:11 final size:12
Alignment explanation
Indices: 955163--955199 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
955153 AAACAAAAAA
955163 AAATGAAAATG-
1 AAATGAAAATGC
955174 AAATGAAAATGC
1 AAATGAAAATGC
*
955186 AAATG-CAATGC
1 AAATGAAAATGC
955197 AAA
1 AAA
955200 CAGAAGGTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 19 0.79
12 5 0.21
ACGTcount: A:0.59, C:0.08, G:0.16, T:0.16
Consensus pattern (12 bp):
AAATGAAAATGC
Found at i:955184 original size:17 final size:17
Alignment explanation
Indices: 955162--955195 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
955152 GAAACAAAAA
955162 AAAATGAAAATGAAATG
1 AAAATGAAAATGAAATG
* *
955179 AAAATGCAAATGCAATG
1 AAAATGAAAATGAAATG
955196 CAAACAGAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.06, G:0.18, T:0.18
Consensus pattern (17 bp):
AAAATGAAAATGAAATG
Found at i:963195 original size:4 final size:4
Alignment explanation
Indices: 963188--963220 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
963178 ACACACACAA
963188 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
963221 TATATACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:964533 original size:391 final size:391
Alignment explanation
Indices: 963804--964630 Score: 1375
Period size: 391 Copynumber: 2.1 Consensus size: 391
963794 TTTAGTATAA
* *
963804 TTTTATTAGGTCATTCGGCTATTAAAAGTTACAAAACAGTCATCCGACTATAGAGTGTTGTTTTG
1 TTTTATTAAGTCACTCGGCTATTAAAAGTTACAAAACAGTCATCCGACTATAGAGTGTTGTTTTG
* *
963869 TTGAGTCACTCAACTATTAAAAGTTACAGAATGGTCACCCAATTATTTATTATGTTCCAAACCCA
66 TTGAGTCACTCAACTATTAAAAGTTACAAAATGGTCACCCAACTATTTATTATGTTCCAAACCCA
* *
963934 TCATTTTTCATTAAAAATGTACAGTATTTTGAGCTGAACGTTAATCTGTTGACTGCGATATGATA
131 TCATTTTTCATTAAAAATGGACAGTATTTTGAGCTGAACATTAATCTGTTGACTGCGATATGATA
*
963999 AAATTTGATACTAAAATCTCAAACGATTATCATATCTCATTCATCATGTTGACATCAAACTTAAA
196 AAATATGATACTAAAATCTCAAACGATTATCATATCTCATTCATCATGTTGACATCAAACTTAAA
* * *
964064 CAATCGTCAAATTTTTAACAGAAAATGACAAGTTTAAAACATAATGAACAGTTGAATGATCATTT
261 CAACCGTCAAATTTTTAACAAAAAATGACAAGTTTAAAACATAATGAACAGTTGAATGACCATTT
* * *
964129 TGGAACTTTTTATAGTCAAGGGATTTAATAAAACAACATTCTATAGTTAGAGTATAATTATGTAA
326 TGGAACATTTTATAGTCAAGAGATTTAATAAAACAACATTCTATAGTTAGAGGATAATTATGTAA
964194 C
391 C
*
964195 TTTTATTAAGTCACTCGACTATTAAAAGTTACAAAACAGTCATCCGACTATAGAGTGTTGTTTTG
1 TTTTATTAAGTCACTCGGCTATTAAAAGTTACAAAACAGTCATCCGACTATAGAGTGTTGTTTTG
* * * *
964260 TTGAGTCCCTCAACTATTAAAAGTTACAAAATGGTCACCCGACTATTTATTATGTTTCAAACTCA
66 TTGAGTCACTCAACTATTAAAAGTTACAAAATGGTCACCCAACTATTTATTATGTTCCAAACCCA
* *
964325 TCATTTTTCATTAAAAATGGACAGTATTTTGAGCTGAACATTAATCTGTTGATTGTGATATGATA
131 TCATTTTTCATTAAAAATGGACAGTATTTTGAGCTGAACATTAATCTGTTGACTGCGATATGATA
* * *
964390 AAATATGATACTAGAATCTCAAATGATTATCATATCTCATTCATCATGTTGACATCCAACTTAAA
196 AAATATGATACTAAAATCTCAAACGATTATCATATCTCATTCATCATGTTGACATCAAACTTAAA
* * * * *
964455 CAACCGTCAATTTTTTAACAAAAAATGACGAGTTTGAAACATAATGAATAGTTGGATGACCATTT
261 CAACCGTCAAATTTTTAACAAAAAATGACAAGTTTAAAACATAATGAACAGTTGAATGACCATTT
* *
964520 TGTAACATTTTATAGTCAAGAGATTTAATAAAGCAACATTCTATAGTTAGAGGATAATTATGTAA
326 TGGAACATTTTATAGTCAAGAGATTTAATAAAACAACATTCTATAGTTAGAGGATAATTATGTAA
964585 C
391 C
*
964586 TTTTATTAAGTCACTCGGCTATTAAAAGTTACAAAACATTCATCC
1 TTTTATTAAGTCACTCGGCTATTAAAAGTTACAAAACAGTCATCC
964631 TCCCAAAATT
Statistics
Matches: 404, Mismatches: 32, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
391 404 1.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (391 bp):
TTTTATTAAGTCACTCGGCTATTAAAAGTTACAAAACAGTCATCCGACTATAGAGTGTTGTTTTG
TTGAGTCACTCAACTATTAAAAGTTACAAAATGGTCACCCAACTATTTATTATGTTCCAAACCCA
TCATTTTTCATTAAAAATGGACAGTATTTTGAGCTGAACATTAATCTGTTGACTGCGATATGATA
AAATATGATACTAAAATCTCAAACGATTATCATATCTCATTCATCATGTTGACATCAAACTTAAA
CAACCGTCAAATTTTTAACAAAAAATGACAAGTTTAAAACATAATGAACAGTTGAATGACCATTT
TGGAACATTTTATAGTCAAGAGATTTAATAAAACAACATTCTATAGTTAGAGGATAATTATGTAA
C
Found at i:970679 original size:32 final size:32
Alignment explanation
Indices: 970609--970669 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
970599 GGAAAACCCG
970609 ACGTCTTTAGTAGAAAACGCTAGAAAGACACA
1 ACGTCTTTAGTAGAAAACGCTAGAAAGACACA
*
970641 ACGTCTTTGGTAGAAAACGCTAGAAAGAC
1 ACGTCTTTAGTAGAAAACGCTAGAAAGAC
970670 GCGAAGTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.20
Consensus pattern (32 bp):
ACGTCTTTAGTAGAAAACGCTAGAAAGACACA
Found at i:970873 original size:2 final size:2
Alignment explanation
Indices: 970866--970894 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
970856 ATATTACACA
970866 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 A
970895 GGGAGCAACT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:972446 original size:27 final size:27
Alignment explanation
Indices: 972377--972435 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
972367 TGAAGCAATA
972377 GTGATGGCAGAGTTCAATTACTGTTGT
1 GTGATGGCAGAGTTCAATTACTGTTGT
972404 GTGATGGCAGAGTTCAATTACTGTTGT
1 GTGATGGCAGAGTTCAATTACTGTTGT
*
972431 TTGAT
1 GTGAT
972436 TGTAGATTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.22, C:0.10, G:0.29, T:0.39
Consensus pattern (27 bp):
GTGATGGCAGAGTTCAATTACTGTTGT
Found at i:977174 original size:14 final size:15
Alignment explanation
Indices: 977117--977183 Score: 84
Period size: 15 Copynumber: 4.5 Consensus size: 15
977107 ATACATTAAT
*
977117 TAAATAATTTAAATATC
1 TAAAAAATTTAAA-A-C
*
977134 TAAAATATTTAAAAC
1 TAAAAAATTTAAAAC
977149 TAAAAAATTTAAAAC
1 TAAAAAATTTAAAAC
977164 TAAAAAA-TTAAAA-
1 TAAAAAATTTAAAAC
977177 TAAAAAA
1 TAAAAAA
977184 ATGTCGACTG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
13 7 0.15
14 6 0.13
15 22 0.47
16 1 0.02
17 11 0.23
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAAAAATTTAAAAC
Found at i:977184 original size:14 final size:15
Alignment explanation
Indices: 977142--977185 Score: 65
Period size: 14 Copynumber: 3.1 Consensus size: 15
977132 TCTAAAATAT
*
977142 TTAAAACTAAAAAAT
1 TTAAAACTAAAAAAA
977157 TTAAAACT-AAAAAA
1 TTAAAACTAAAAAAA
977171 TTAAAA-TAAAAAAA
1 TTAAAACTAAAAAAA
977185 T
1 T
977186 GTCGACTGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 1 0.04
14 18 0.67
15 8 0.30
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (15 bp):
TTAAAACTAAAAAAA
Found at i:978328 original size:53 final size:54
Alignment explanation
Indices: 978227--978331 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 54
978217 AAGTTAAAAA
*
978227 ATTAAGTTAATCGAATTAATAATTTTTTATTTTATAATTTAAATTTATTGGAAT
1 ATTAAGTTAATCGAATCAATAATTTTTTATTTTATAATTTAAATTTATTGGAAT
978281 ATTAAGTTAATCGAATCAATAA-TTTTTATTTTATAATTTAAATTTATTGGA
1 ATTAAGTTAATCGAATCAATAATTTTTTATTTTATAATTTAAATTTATTGGA
978332 TTTTTTAAAG
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
53 29 0.58
54 21 0.42
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (54 bp):
ATTAAGTTAATCGAATCAATAATTTTTTATTTTATAATTTAAATTTATTGGAAT
Found at i:987004 original size:2 final size:2
Alignment explanation
Indices: 986999--987023 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
986989 TTTTGACCTG
986999 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 A
987024 AAGAAAAATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:989286 original size:22 final size:24
Alignment explanation
Indices: 989261--989306 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
989251 ACAAGTAAGC
989261 ATTTA-GT-TTACTTTTTTTTTAA
1 ATTTAGGTATTACTTTTTTTTTAA
*
989283 ATTTAGGTGATTGCTTTTTTTTTA
1 ATTTAGGT-ATTACTTTTTTTTTA
989307 TTTTACGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 2 0.10
25 13 0.65
ACGTcount: A:0.20, C:0.04, G:0.11, T:0.65
Consensus pattern (24 bp):
ATTTAGGTATTACTTTTTTTTTAA
Found at i:992948 original size:17 final size:18
Alignment explanation
Indices: 992899--992948 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
992889 AGAATATGTA
*
992899 TCATATCAATTAAATCAT
1 TCATATCAATTAAATCAG
*
992917 TC-CATCAATCT-AATC-G
1 TCATATCAAT-TAAATCAG
992933 TCATATCAATTAAATC
1 TCATATCAATTAAATC
992949 TATCATAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 7
0.72 0.08 0.19
Matches are distributed among these distances:
16 3 0.12
17 20 0.77
18 3 0.12
ACGTcount: A:0.40, C:0.22, G:0.02, T:0.36
Consensus pattern (18 bp):
TCATATCAATTAAATCAG
Found at i:994080 original size:19 final size:20
Alignment explanation
Indices: 994037--994079 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
994027 TTATTTTTTA
994037 TTTTT-ATTTTAAAATTATC
1 TTTTTAATTTTAAAATTATC
994056 TTTTTAATTTT-AAATGTATC
1 TTTTTAATTTTAAAAT-TATC
994076 TTTT
1 TTTT
994080 AGGGTTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTTAATTTTAAAATTATC
Found at i:1006547 original size:15 final size:16
Alignment explanation
Indices: 1006518--1006550 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1006508 GAATTGATTA
1006518 TAATTATATAATTTCAT
1 TAATTATAT-ATTTCAT
1006535 TAATTATAT-TTTCAT
1 TAATTATATATTTCAT
1006550 T
1 T
1006551 CAGATCATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
TAATTATATATTTCAT
Found at i:1008019 original size:21 final size:21
Alignment explanation
Indices: 1007968--1008024 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
1007958 AGAGAATTTG
* *
1007968 ATAATTATAAAAATAATACTT
1 ATAATTATATATATAATACTT
*
1007989 ATAAATATATATATAATACTT
1 ATAATTATATATATAATACTT
1008010 ATAATTATATATATA
1 ATAATTATATATATA
1008025 TATATATAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
ATAATTATATATATAATACTT
Found at i:1010611 original size:2 final size:2
Alignment explanation
Indices: 1010604--1010653 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1010594 AGCATTCATA
1010604 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1010646 AT AT AT AT
1 AT AT AT AT
1010654 TGACTCATAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1017581 original size:217 final size:225
Alignment explanation
Indices: 1017170--1017616 Score: 651
Period size: 217 Copynumber: 2.0 Consensus size: 225
1017160 TTTTTTCTTT
*
1017170 TCTTTATAATGTATCTCTATTTTCTTTTATTTTTTTTTATTTTCAATAAGTCTGTTGGTATGACA
1 TCTTTATAATGTATCTCTATTTTCTTTTA----TTTTTATTTTCAATAAGTCTGTTGATATGACA
* * *
1017235 CGTTTTCATTTGTCTTTATGACATGTTTTCTTATTTTTTTAGCATGTTTTATGGTTATTTGGCAT
62 CGTTTTCATTTGTCTTTATGACACGTTTTCTTATTTTGTTAGCATGTTTTATGGTTAGTTGGCAT
*
1017300 TTTTTTCATTTATATTTTTTAAGTGTTGATTTGACATTGCCACGTATGATTAAGATGACGTTTAT
127 TTTTTTCATTTATATTTTTTAAGGGTTGATTTGACATTGCCACGTATGATTAAGATGACGTTTAT
* *
1017365 CTGATATCATATTGATCTTCCCTAATTTGGACTC
192 ATAATATCATATTGATCTTCCCTAATTTGGACTC
* * *
1017399 TCTTTTTATTGTATCTCTATTTTCTTTTA-TTTT-TTTTCAATAAGTTTGTTGATATGACACGTT
1 TCTTTATAATGTATCTCTATTTTCTTTTATTTTTATTTTCAATAAGTCTGTTGATATGACACGTT
*
1017462 TTCATTTGTCTTTATGACACG-TTT-TT-TTTTGTT-GCATGTTTTATGGATT-GTTGGCCTTTT
66 TTCATTTGTCTTTATGACACGTTTTCTTATTTTGTTAGCATGTTTTATGG-TTAGTTGGCATTTT
* *
1017522 TTTCA-TT-TATTTTTTAAGGGTTGATTTGACATTGCTATGTATGATTAAGATGACGTTTATATA
130 TTTCATTTATATTTTTTAAGGGTTGATTTGACATTGCCACGTATGATTAAGATGACGTTTATATA
* *
1017585 ATATCATATTGATCTTTCCTGATTTGGACTC
195 ATATCATATTGATCTTCCCTAATTTGGACTC
1017616 T
1 T
1017617 TATATTGGAT
Statistics
Matches: 202, Mismatches: 15, Indels: 14
0.87 0.06 0.06
Matches are distributed among these distances:
217 81 0.40
218 2 0.01
219 27 0.13
220 8 0.04
221 2 0.01
222 3 0.01
223 48 0.24
224 4 0.02
229 27 0.13
ACGTcount: A:0.20, C:0.12, G:0.14, T:0.54
Consensus pattern (225 bp):
TCTTTATAATGTATCTCTATTTTCTTTTATTTTTATTTTCAATAAGTCTGTTGATATGACACGTT
TTCATTTGTCTTTATGACACGTTTTCTTATTTTGTTAGCATGTTTTATGGTTAGTTGGCATTTTT
TTCATTTATATTTTTTAAGGGTTGATTTGACATTGCCACGTATGATTAAGATGACGTTTATATAA
TATCATATTGATCTTCCCTAATTTGGACTC
Found at i:1018533 original size:2 final size:2
Alignment explanation
Indices: 1018526--1018552 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1018516 CTATAAACGA
1018526 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 A
1018553 AAATAAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1020584 original size:2 final size:2
Alignment explanation
Indices: 1020577--1020606 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1020567 AGATTATTAG
1020577 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
1020607 TATTTTTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1039310 original size:2 final size:2
Alignment explanation
Indices: 1039303--1039329 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1039293 ATCAGACAAG
1039303 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 A
1039330 GAATAGTCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1049437 original size:2 final size:2
Alignment explanation
Indices: 1049430--1049501 Score: 84
Period size: 2 Copynumber: 39.0 Consensus size: 2
1049420 CCGCCCCGAT
1049430 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1049471 T- TT TA TA TA T- TT TA TA TA T- TA -A T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1049502 ATACAAACAA
Statistics
Matches: 62, Mismatches: 2, Indels: 12
0.82 0.03 0.16
Matches are distributed among these distances:
1 6 0.10
2 56 0.90
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:1051713 original size:18 final size:17
Alignment explanation
Indices: 1051690--1051753 Score: 83
Period size: 18 Copynumber: 3.6 Consensus size: 17
1051680 TATGAAATTG
1051690 GATTCCAATTCATTCACA
1 GATTCCAATTC-TTCACA
* *
1051708 GATTCCAATTCCTGACA
1 GATTCCAATTCTTCACA
*
1051725 GATTCTAATTTCTTCACA
1 GATTCCAA-TTCTTCACA
1051743 GATTCCAATTC
1 GATTCCAATTC
1051754 CCTCATAAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
17 14 0.36
18 25 0.64
ACGTcount: A:0.30, C:0.27, G:0.08, T:0.36
Consensus pattern (17 bp):
GATTCCAATTCTTCACA
Found at i:1061909 original size:3 final size:3
Alignment explanation
Indices: 1061901--1061952 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
1061891 GCTTTTAATG
1061901 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1061949 AGA A
1 AGA A
1061953 ATTGTACTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1068727 original size:5 final size:5
Alignment explanation
Indices: 1068717--1068742 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1068707 TGACTTAGAA
1068717 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
1068743 AATAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:1083894 original size:21 final size:21
Alignment explanation
Indices: 1083868--1083909 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1083858 AAATATAACC
1083868 TAATAAAAAATTTAAA-AATAT
1 TAAT-AAAAATTTAAATAATAT
*
1083889 TAATAATAATTTAAATAATAT
1 TAATAAAAATTTAAATAATAT
1083910 AATTTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAATAAAAATTTAAATAATAT
Found at i:1085295 original size:28 final size:28
Alignment explanation
Indices: 1085264--1085326 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
1085254 AACATGAACC
1085264 TGTAACTTCTACGAATAACAACAATTCA
1 TGTAACTTCTACGAATAACAACAATTCA
*
1085292 TGTAACTTCTACGAATAATAACAATTCA
1 TGTAACTTCTACGAATAACAACAATTCA
*
1085320 TTTAACT
1 TGTAACT
1085327 ACCGAGATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.33
Consensus pattern (28 bp):
TGTAACTTCTACGAATAACAACAATTCA
Found at i:1088720 original size:37 final size:38
Alignment explanation
Indices: 1088668--1088766 Score: 114
Period size: 37 Copynumber: 2.7 Consensus size: 38
1088658 CGTTTTTAAA
* * *
1088668 AAAACATATATTATATAGTTTTGAAAACACG-TTTTCG
1 AAAACGTATAATATATAGTTTTGAAAAAACGATTTTCG
**
1088705 AAAACGTATAATATATAGTTTT-AAAAAACGATTTTTT
1 AAAACGTATAATATATAGTTTTGAAAAAACGATTTTCG
*
1088742 AAAAGGTAT-ATAATATAGTTTTGAA
1 AAAACGTATAAT-ATATAGTTTTGAA
1088767 TATATATATA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
36 9 0.17
37 42 0.79
38 2 0.04
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.38
Consensus pattern (38 bp):
AAAACGTATAATATATAGTTTTGAAAAAACGATTTTCG
Found at i:1088771 original size:2 final size:2
Alignment explanation
Indices: 1088766--1088792 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1088756 ATAGTTTTGA
1088766 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 A
1088793 GTTTTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1088865 original size:16 final size:16
Alignment explanation
Indices: 1088827--1088932 Score: 79
Period size: 16 Copynumber: 7.0 Consensus size: 16
1088817 ACATATATAC
* *
1088827 TATATATTATATAATGT
1 TATATATTAT-TTATTT
1088844 TA-ATATTATTTATTT
1 TATATATTATTTATTT
1088859 TATATATTA-TTA-TT
1 TATATATTATTTATTT
1088873 TATATATTA--TA--T
1 TATATATTATTTATTT
1088885 TA-ATATTATTTATTAT
1 TATATATTATTTATT-T
*
1088901 TAT-T-TGTATTTATATA
1 TATATAT-TATTTAT-TT
1088917 TATATATTATTTATTT
1 TATATATTATTTATTT
1088933 ATTGTCTTAT
Statistics
Matches: 74, Mismatches: 4, Indels: 23
0.73 0.04 0.23
Matches are distributed among these distances:
11 6 0.08
12 3 0.04
13 4 0.05
14 11 0.15
15 10 0.14
16 28 0.38
17 11 0.15
18 1 0.01
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (16 bp):
TATATATTATTTATTT
Found at i:1088923 original size:44 final size:43
Alignment explanation
Indices: 1088819--1088926 Score: 120
Period size: 41 Copynumber: 2.6 Consensus size: 43
1088809 TTTAAGAAAC
* * *
1088819 ATATA-TACTATATAT-TATATAATGTTAATATTATTTATTTT
1 ATATATTATTATATATATATATTATATTAATATTATTTATTTT
1088860 ATATATTATTAT-T-TATATATTATATTAATATTATTTATTATT
1 ATATATTATTATATATATATATTATATTAATATTATTTATT-TT
1088902 AT-T-TGTATTTATATATATATATTAT
1 ATATAT-TA-TTATATATATATATTAT
1088927 TTATTTATTG
Statistics
Matches: 57, Mismatches: 3, Indels: 11
0.80 0.04 0.15
Matches are distributed among these distances:
40 2 0.04
41 31 0.54
42 13 0.23
43 1 0.02
44 10 0.18
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (43 bp):
ATATATTATTATATATATATATTATATTAATATTATTTATTTT
Found at i:1088944 original size:33 final size:31
Alignment explanation
Indices: 1088858--1088944 Score: 86
Period size: 32 Copynumber: 2.7 Consensus size: 31
1088848 ATTATTTATT
* * *
1088858 TTATATATTATTATTTATATATTATATTAATA
1 TTATTTATTATTATCTGTAT-TTATATTAATA
*
1088890 TTATTTATTATTATTTGTATTTATATATATATA
1 TTATTTATTATTATCTGTATTTATAT-TA-ATA
*
1088923 TTATTTATTTATTGTCT-TATTT
1 TTATTTA-TTATTATCTGTATTT
1088945 TTGTTTTTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
31 6 0.12
32 20 0.42
33 15 0.31
34 7 0.15
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.64
Consensus pattern (31 bp):
TTATTTATTATTATCTGTATTTATATTAATA
Found at i:1090223 original size:39 final size:38
Alignment explanation
Indices: 1090141--1090272 Score: 124
Period size: 45 Copynumber: 3.2 Consensus size: 38
1090131 TTATATTATT
* *
1090141 TTTATTTCTTCTAAAATTT-ATATTTCTTTC-TCTTTTCA
1 TTTATTTCTTTTAAAATTTAATATTTC-TTCAT-TTTTTA
1090179 TTTTATTTCTTTTAAAATTTAATATTTGCTTCATTTTTTA
1 -TTTATTTCTTTTAAAATTTAATATTT-CTTCATTTTTTA
*
1090219 TTTATTTTAAATTCTTTTAAAATTTAACATTTTCTTCATTTTTTA
1 TTTA---T---TTCTTTTAAAATTTAATA-TTTCTTCATTTTTTA
1090264 TTTATTTCT
1 TTTATTTCT
1090273 CTTTTAATAT
Statistics
Matches: 80, Mismatches: 3, Indels: 20
0.78 0.03 0.19
Matches are distributed among these distances:
39 26 0.32
40 14 0.17
41 2 0.03
42 2 0.03
45 33 0.41
46 3 0.04
ACGTcount: A:0.24, C:0.11, G:0.01, T:0.64
Consensus pattern (38 bp):
TTTATTTCTTTTAAAATTTAATATTTCTTCATTTTTTA
Found at i:1090235 original size:45 final size:45
Alignment explanation
Indices: 1090185--1090270 Score: 154
Period size: 45 Copynumber: 1.9 Consensus size: 45
1090175 TTCATTTTAT
*
1090185 TTCTTTTAAAATTTAATATTTGCTTCATTTTTTATTTATTTTAAA
1 TTCTTTTAAAATTTAACATTTGCTTCATTTTTTATTTATTTTAAA
*
1090230 TTCTTTTAAAATTTAACATTTTCTTCATTTTTTATTTATTT
1 TTCTTTTAAAATTTAACATTTGCTTCATTTTTTATTTATTT
1090271 CTCTTTTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.27, C:0.08, G:0.01, T:0.64
Consensus pattern (45 bp):
TTCTTTTAAAATTTAACATTTGCTTCATTTTTTATTTATTTTAAA
Found at i:1090298 original size:13 final size:13
Alignment explanation
Indices: 1090280--1090327 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
1090270 TCTCTTTTAA
1090280 TATTATTTTACTT
1 TATTATTTTACTT
*
1090293 TATTATTGTTTCTT
1 TATTATT-TTACTT
1090307 T-TTATTTTAACTT
1 TATTATTTT-ACTT
1090320 TATT-TTTT
1 TATTATTTT
1090328 CTTATTTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
12 2 0.07
13 20 0.67
14 8 0.27
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.73
Consensus pattern (13 bp):
TATTATTTTACTT
Found at i:1096679 original size:126 final size:127
Alignment explanation
Indices: 1096447--1096691 Score: 379
Period size: 126 Copynumber: 1.9 Consensus size: 127
1096437 ACAAAGGGAG
* *
1096447 AGAGATAGAGAAGCTGCTCGGATCGCAGTGGAAAGTATGAAAAACACAGCTGGAGTTGAAATTAA
1 AGAGATAGAGAAGCTGCTCGGATAGCAGTGGAAAGTATGAAAAACACAGCGGGAGTTGAAATTAA
* * *
1096512 TTTAGATGCTGAAAGGGAATTCAATTTCCTCGTAGGGTCTTCTTCTTCCTTAATCCATCGGA
66 TTTAGAAGCTGAAAGGGAATTCAATTTCCTCATAGGATCTTCTTCTTCCTTAATCCATCGGA
* * *
1096574 AGAGATAGAGAATCTGCTCGGATATCATTGGAAAGTATG-AAAACACAGCGGG-GATTGAAATTA
1 AGAGATAGAGAAGCTGCTCGGATAGCAGTGGAAAGTATGAAAAACACAGCGGGAG-TTGAAATTA
1096637 ATTTAGAAGCTGAAAGGGAATTCAATATT-CTCATAGGATCTTCTTCTTCCTTAAT
65 ATTTAGAAGCTGAAAGGGAATTCAAT-TTCCTCATAGGATCTTCTTCTTCCTTAAT
1096692 GCATAGGATA
Statistics
Matches: 108, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
125 1 0.01
126 70 0.65
127 37 0.34
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (127 bp):
AGAGATAGAGAAGCTGCTCGGATAGCAGTGGAAAGTATGAAAAACACAGCGGGAGTTGAAATTAA
TTTAGAAGCTGAAAGGGAATTCAATTTCCTCATAGGATCTTCTTCTTCCTTAATCCATCGGA
Found at i:1097590 original size:32 final size:32
Alignment explanation
Indices: 1097554--1097639 Score: 93
Period size: 32 Copynumber: 2.7 Consensus size: 32
1097544 ATATCAGATT
* *
1097554 TTTTCAGGTTAGGTCAATATCAAATCGATTAA
1 TTTTCGGGTTAGATCAATATCAAATCGATTAA
* * * * *
1097586 TTTTCGGGTCATATTAATATCAAATCGTTTAG
1 TTTTCGGGTTAGATCAATATCAAATCGATTAA
1097618 TTTTCGGGTT-GAATCAATATCA
1 TTTTCGGGTTAG-ATCAATATCA
1097640 TATTGGTTGA
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (32 bp):
TTTTCGGGTTAGATCAATATCAAATCGATTAA
Found at i:1098032 original size:5 final size:5
Alignment explanation
Indices: 1098022--1098047 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1098012 ATTATTTTTC
1098022 AATTT AATTT AATTT AATTT AATTT A
1 AATTT AATTT AATTT AATTT AATTT A
1098048 TTATTCAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
AATTT
Found at i:1098351 original size:22 final size:22
Alignment explanation
Indices: 1098326--1098367 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1098316 AATTTCATTT
*
1098326 ATATAAAAAAAATTATATATCA
1 ATATAAAAAAAATAATATATCA
* *
1098348 ATATAATAATAATAATATAT
1 ATATAAAAAAAATAATATAT
1098368 TCTTTATAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
ATATAAAAAAAATAATATATCA
Found at i:1098780 original size:16 final size:16
Alignment explanation
Indices: 1098735--1098773 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1098725 ATCGGTTTTA
*
1098735 TTTAGTTCGGGTTACT
1 TTTAGTTCGAGTTACT
*
1098751 TTCAGTTCGAGTTACT
1 TTTAGTTCGAGTTACT
1098767 TTTAGTT
1 TTTAGTT
1098774 TGTGTTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.21, T:0.51
Consensus pattern (16 bp):
TTTAGTTCGAGTTACT
Found at i:1099921 original size:126 final size:126
Alignment explanation
Indices: 1099696--1099935 Score: 383
Period size: 126 Copynumber: 1.9 Consensus size: 126
1099686 GGAAGAGAAT
* * *
1099696 TAGAGAAGCTGCTCGGATCGCAGTGGAAAGTATGAAAAACACAGCTGGAATTGAAATTAATTTAG
1 TAGAGAAGCTGCTCGGATCGCAGTGGAAAGCAAGAAAAACACAGCGGGAATTGAAATTAATTTAG
** *
1099761 ATTCTGAAAGGGAATTCAATTTCCTCGTAGGATCTTCTTCTTCCTTAATCCATCGGAAAGA
66 AGGCTGAAAGGGAATTCAATTTCCTCATAGGATCTTCTTCTTCCTTAATCCATCGGAAAGA
* * *
1099822 TAGAGAAGCTGCTCGGATGGCATTGGAAAGCAAGAAAAACACAGCGGGGATTGAAATTAATTTAG
1 TAGAGAAGCTGCTCGGATCGCAGTGGAAAGCAAGAAAAACACAGCGGGAATTGAAATTAATTTAG
1099887 AGGCTGAAAGGGAATTCAATATT-CTCATAGGATCTTCTTCTTCCTTAAT
66 AGGCTGAAAGGGAATTCAAT-TTCCTCATAGGATCTTCTTCTTCCTTAAT
1099936 GCATAGGATA
Statistics
Matches: 104, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
126 102 0.98
127 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.28
Consensus pattern (126 bp):
TAGAGAAGCTGCTCGGATCGCAGTGGAAAGCAAGAAAAACACAGCGGGAATTGAAATTAATTTAG
AGGCTGAAAGGGAATTCAATTTCCTCATAGGATCTTCTTCTTCCTTAATCCATCGGAAAGA
Found at i:1100736 original size:17 final size:17
Alignment explanation
Indices: 1100711--1100751 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
1100701 GTCGGGTCGA
*
1100711 GTCGAGTCAATTTTCAG
1 GTCGGGTCAATTTTCAG
*
1100728 GTCGGGTCAATTTTCGG
1 GTCGGGTCAATTTTCAG
1100745 GTCGGGT
1 GTCGGGT
1100752 GATAATTGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.15, C:0.17, G:0.34, T:0.34
Consensus pattern (17 bp):
GTCGGGTCAATTTTCAG
Found at i:1101794 original size:21 final size:21
Alignment explanation
Indices: 1101765--1101813 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
1101755 AGCTGAAGCG
1101765 AGAGAAGCAGAGACAGAAGCAA
1 AGAG-AGCAGAGACAGAAGCAA
** * *
1101787 AGAGAGCATCGAGAGAAGCAG
1 AGAGAGCAGAGACAGAAGCAA
1101808 AGAGAG
1 AGAGAG
1101814 AAGCAACATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.49, C:0.12, G:0.37, T:0.02
Consensus pattern (21 bp):
AGAGAGCAGAGACAGAAGCAA
Found at i:1101812 original size:12 final size:12
Alignment explanation
Indices: 1101764--1101818 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
1101754 AAGCTGAAGC
1101764 GAGAGAAGCAGA
1 GAGAGAAGCAGA
*
1101776 GACAGAAGCA-A
1 GAGAGAAGCAGA
**
1101787 -AGAG-AGCATC
1 GAGAGAAGCAGA
1101797 GAGAGAAGCAGA
1 GAGAGAAGCAGA
1101809 GAGAGAAGCA
1 GAGAGAAGCA
1101819 ACATTTTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
9 4 0.11
10 3 0.09
11 5 0.14
12 23 0.66
ACGTcount: A:0.49, C:0.13, G:0.36, T:0.02
Consensus pattern (12 bp):
GAGAGAAGCAGA
Found at i:1105721 original size:16 final size:16
Alignment explanation
Indices: 1105695--1105732 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
1105685 TCTACTAAAG
1105695 CATGATTGGGTAGATAT
1 CATG-TTGGGTAGATAT
1105712 CATGTTGGGTAGATAT
1 CATGTTGGGTAGATAT
1105728 CATGT
1 CATGT
1105733 GAATAAGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.26, C:0.08, G:0.29, T:0.37
Consensus pattern (16 bp):
CATGTTGGGTAGATAT
Found at i:1112181 original size:12 final size:12
Alignment explanation
Indices: 1112164--1112190 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1112154 CCTATGTATA
1112164 TATGTATATATG
1 TATGTATATATG
1112176 TATGTATATATG
1 TATGTATATATG
1112188 TAT
1 TAT
1112191 ATCTTCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (12 bp):
TATGTATATATG
Found at i:1115690 original size:7 final size:8
Alignment explanation
Indices: 1115673--1115728 Score: 59
Period size: 8 Copynumber: 7.5 Consensus size: 8
1115663 AAAATGAGTG
1115673 AAAATGAA
1 AAAATGAA
1115681 AAAATGAAA
1 AAAATG-AA
*
1115690 AAAATAAA
1 AAAATGAA
1115698 AAAAT-AA
1 AAAATGAA
1115705 AAAATG--
1 AAAATGAA
1115711 --AATGAA
1 AAAATGAA
1115717 AAAATGAA
1 AAAATGAA
1115725 AAAA
1 AAAA
1115729 ATGAGGGTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
4 4 0.10
7 7 0.17
8 23 0.56
9 7 0.17
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (8 bp):
AAAATGAA
Found at i:1115693 original size:9 final size:9
Alignment explanation
Indices: 1115673--1115732 Score: 72
Period size: 9 Copynumber: 6.8 Consensus size: 9
1115663 AAAATGAGTG
1115673 AAAATG-AA
1 AAAATGAAA
1115681 AAAATGAAA
1 AAAATGAAA
1115690 AAAAT-AAA
1 AAAATGAAA
*
1115698 AAAATAAAA
1 AAAATGAAA
1115707 AATGAATG-AA
1 AA--AATGAAA
1115717 AAAATGAAA
1 AAAATGAAA
1115726 AAAATGA
1 AAAATGA
1115733 GGGTTCAAGA
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
8 18 0.39
9 21 0.46
10 4 0.09
11 3 0.07
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (9 bp):
AAAATGAAA
Found at i:1116994 original size:166 final size:165
Alignment explanation
Indices: 1116721--1117059 Score: 563
Period size: 166 Copynumber: 2.0 Consensus size: 165
1116711 CAGCGATCGT
**
1116721 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCGACTGTTGAAGATTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACAAGACTGTTGAAGATTGT
*
1116786 TCGAGTCTTATACTCTCTGCAGAAATAGGGAGCAGACACGATTGATGAAGATTGTTCGAGTCTTA
66 TCGAGTCTTATACTCTCTGCAGAAATAGGGAGCAGACACGATTGATGAAGATTGTTCAAGTCTTA
* *
1116851 TACTCTCTGAAGGAATGGGGAGTAGACACGATTGA
131 TACTCTCTGAAGGAAGGGGGAGCAGACACGATTGA
* * *
1116886 TGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGATAAGATTGGTTGAAGATTG
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACAAGACT-GTTGAAGATTG
* *
1116951 TTTGGGTCTTATACTCTCTG-AGGAAATAGGGAGCAGACACGATTGATGAAGATTGTTCAAGTCT
65 TTCGAGTCTTATACTCTCTGCA-GAAATAGGGAGCAGACACGATTGATGAAGATTGTTCAAGTCT
1117015 TATACTCTCTGAAGGAAGGGGGAGCAGACACGATTGA
129 TATACTCTCTGAAGGAAGGGGGAGCAGACACGATTGA
1117052 TGAAGATT
1 TGAAGATT
1117060 CTTCAAGTTC
Statistics
Matches: 162, Mismatches: 10, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
165 49 0.30
166 113 0.70
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (165 bp):
TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACAAGACTGTTGAAGATTGT
TCGAGTCTTATACTCTCTGCAGAAATAGGGAGCAGACACGATTGATGAAGATTGTTCAAGTCTTA
TACTCTCTGAAGGAAGGGGGAGCAGACACGATTGA
Found at i:1117067 original size:55 final size:55
Alignment explanation
Indices: 1116721--1117059 Score: 507
Period size: 55 Copynumber: 6.1 Consensus size: 55
1116711 CAGCGATCGT
* * *
1116721 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACGCGACTGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
*
1116776 TGAAGATTGTTCGAGTCTTATACTCTCTGCAGAAATAGGGAGCAGACACGATTGA
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
* * *
1116831 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATGGGGAGTAGACACGATTGA
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
* * * *
1116886 TGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGATAAGATTGGT
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATT-GA
* * *
1116942 TGAAGATTGTTTGGGTCTTATACTCTCTGAGGAAATAGGGAGCAGACACGATTGA
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
* * **
1116997 TGAAGATTGTTCAAGTCTTATACTCTCTGAAGGAAGGGGGAGCAGACACGATTGA
1 TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
1117052 TGAAGATT
1 TGAAGATT
1117060 CTTCAAGTTC
Statistics
Matches: 256, Mismatches: 27, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
55 206 0.80
56 50 0.20
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (55 bp):
TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGA
Found at i:1120507 original size:16 final size:16
Alignment explanation
Indices: 1120483--1120520 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1120473 GTTTATATTT
*
1120483 AGTTCGAGTTACTTTC
1 AGTTTGAGTTACTTTC
*
1120499 AGTTTGAGTTACTTTT
1 AGTTTGAGTTACTTTC
1120515 AGTTTG
1 AGTTTG
1120521 TGCTATTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.18, C:0.11, G:0.21, T:0.50
Consensus pattern (16 bp):
AGTTTGAGTTACTTTC
Found at i:1121715 original size:129 final size:129
Alignment explanation
Indices: 1121478--1121727 Score: 412
Period size: 129 Copynumber: 1.9 Consensus size: 129
1121468 AAACAACGGG
* *
1121478 AGAGAGATAGAGAAGCTGCTCGGATGGCATTGGAAAGTATGAAAAACACAGCTGGGATTGAAATT
1 AGAGAGATAGAGAAGCTGCTCGGATAGCATTGGAAAGTATGAAAAACACAGCGGGGATTGAAATT
* * *
1121543 AATTTAGATGCTGAAAGGGAATTCAATTTCCTCGTAGGGTCTTCTTCTTCCTTAATCCATCGGA
66 AATTTAGAAGCTGAAAGGGAATTCAATTTCCTCATAGGATCTTCTTCTTCCTTAATCCATCGGA
* *
1121607 AGAGAGATAGAGAATCTGCTCGGATATCATTGGAAAGTATGAAAAACACAGCGGGGATTGAAATT
1 AGAGAGATAGAGAAGCTGCTCGGATAGCATTGGAAAGTATGAAAAACACAGCGGGGATTGAAATT
*
1121672 AATTTAGAAGCTGAAAGGGAATTCAATATT-TTCATAGGATCTTCTTCTTCCTTAAT
66 AATTTAGAAGCTGAAAGGGAATTCAAT-TTCCTCATAGGATCTTCTTCTTCCTTAAT
1121728 GCATAGGATA
Statistics
Matches: 112, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
129 110 0.98
130 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (129 bp):
AGAGAGATAGAGAAGCTGCTCGGATAGCATTGGAAAGTATGAAAAACACAGCGGGGATTGAAATT
AATTTAGAAGCTGAAAGGGAATTCAATTTCCTCATAGGATCTTCTTCTTCCTTAATCCATCGGA
Found at i:1122959 original size:17 final size:17
Alignment explanation
Indices: 1122930--1122974 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1122920 TCGGGTCGGG
* *
1122930 TCGAGTCGAGTCAATTT
1 TCGAGTCGGGTCAAATT
1122947 TC-AGGTCGGGTCAAATT
1 TCGA-GTCGGGTCAAATT
1122964 TCGAGTCGGGT
1 TCGAGTCGGGT
1122975 GATAATTGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 1 0.04
17 22 0.92
18 1 0.04
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (17 bp):
TCGAGTCGGGTCAAATT
Found at i:1129510 original size:129 final size:129
Alignment explanation
Indices: 1129278--1129527 Score: 430
Period size: 129 Copynumber: 1.9 Consensus size: 129
1129268 AAACAAAGGG
*
1129278 AGAGAGATAGAGAAGCTGCTCGGATCGCAGTGGAAAGTATGAAAAACACAGCTGGAATTGAAATT
1 AGAGAGATAGAGAAGCTGCTCGGATCGCAGTGGAAAGTATGAAAAACACAGCGGGAATTGAAATT
* *
1129343 AATTTAGATGCTGAAAGGGAATTCAATTTCCTCGTAGGATCTTCTTCTTCCTTAATCCATCGGA
66 AATTTAGAAGCTGAAAGGGAATTCAATTTCCTCATAGGATCTTCTTCTTCCTTAATCCATCGGA
* * *
1129407 AGAGAGATAGAGAAGCTGCTCGGATGGCATTGGAAAGTATGAAAAACACAGCGGGGATTGAAATT
1 AGAGAGATAGAGAAGCTGCTCGGATCGCAGTGGAAAGTATGAAAAACACAGCGGGAATTGAAATT
1129472 AATTTAGAAGCTGAAAGGGAATTCAATATT-CTCATAGGATCTTCTTCTTCCTTAAT
66 AATTTAGAAGCTGAAAGGGAATTCAAT-TTCCTCATAGGATCTTCTTCTTCCTTAAT
1129528 GCATAGGATA
Statistics
Matches: 114, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
129 112 0.98
130 2 0.02
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (129 bp):
AGAGAGATAGAGAAGCTGCTCGGATCGCAGTGGAAAGTATGAAAAACACAGCGGGAATTGAAATT
AATTTAGAAGCTGAAAGGGAATTCAATTTCCTCATAGGATCTTCTTCTTCCTTAATCCATCGGA
Found at i:1130399 original size:17 final size:17
Alignment explanation
Indices: 1130374--1130414 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1130364 GTCGGGTCGA
* *
1130374 GTCGAGTCAATTTTCAG
1 GTCGGGTCAAATTTCAG
*
1130391 GTCGGGTCAAATTTCGG
1 GTCGGGTCAAATTTCAG
1130408 GTCGGGT
1 GTCGGGT
1130415 GATAATTGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.17, C:0.17, G:0.34, T:0.32
Consensus pattern (17 bp):
GTCGGGTCAAATTTCAG
Found at i:1131406 original size:21 final size:21
Alignment explanation
Indices: 1131377--1131453 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
1131367 AGCTGAAGCG
*
1131377 AGAGAAGCAGAGACAGAAGCAA
1 AGAG-AGCAGAGAGAGAAGCAA
**
1131399 AGAGAGCATCGAGAGAAGCAA
1 AGAGAGCAGAGAGAGAAGCAA
** *
1131420 AGAGAGCATCGAGAGAAGCAG
1 AGAGAGCAGAGAGAGAAGCAA
1131441 AGAGAGC-GAGAGA
1 AGAGAGCAGAGAGA
1131454 AGCAGAGAGA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 4 0.08
21 41 0.84
22 4 0.08
ACGTcount: A:0.48, C:0.13, G:0.36, T:0.03
Consensus pattern (21 bp):
AGAGAGCAGAGAGAGAAGCAA
Found at i:1131445 original size:12 final size:12
Alignment explanation
Indices: 1131376--1131469 Score: 61
Period size: 12 Copynumber: 7.8 Consensus size: 12
1131366 AAGCTGAAGC
1131376 GAGAGAAGCAGA
1 GAGAGAAGCAGA
*
1131388 GACAGAAGCA-A
1 GAGAGAAGCAGA
**
1131399 -AGAG-AGCATC
1 GAGAGAAGCAGA
*
1131409 GAGAGAAGCAAA
1 GAGAGAAGCAGA
* *
1131421 GAGAGCATCGAGA
1 GAGAGAAGC-AGA
*
1131434 GAAGCAGAGAG-AGC
1 G-AG-AGA-AGCAGA
1131448 GAGAGAAGCAGA
1 GAGAGAAGCAGA
1131460 GAGAGAAGCA
1 GAGAGAAGCA
1131470 ACATTTTAGA
Statistics
Matches: 62, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
9 4 0.06
10 3 0.05
11 7 0.11
12 35 0.56
13 5 0.08
14 5 0.08
15 2 0.03
16 1 0.02
ACGTcount: A:0.48, C:0.13, G:0.37, T:0.02
Consensus pattern (12 bp):
GAGAGAAGCAGA
Found at i:1133885 original size:129 final size:129
Alignment explanation
Indices: 1133653--1133902 Score: 403
Period size: 129 Copynumber: 1.9 Consensus size: 129
1133643 AAACAAAGGG
* *
1133653 AGAGAGATAGAGAAGCTGCTCGGATCGCAGTGGAAAGTATGAAAAACACAGCTGGAATTGAAATT
1 AGAGAGATAGAGAAGCTGCTCGGATAGCAGTGGAAAGTATGAAAAACACAGCGGGAATTGAAATT
* *
1133718 AATTTAGATGCTGAAAGGGAATTCAATTTCCTCGTAGGATCTTCTTCTTCCTTAATCCATCGGA
66 AATTTAGAAGCTGAAAGGGAATTCAATTTCCTCATAGGATCTTCTTCTTCCTTAATCCATCGGA
* * * *
1133782 AGAGAGATAGAGAATCTGCTCGGATATCATTGGAAAGTATGAAAAACACAGCGGGGATTGAAATT
1 AGAGAGATAGAGAAGCTGCTCGGATAGCAGTGGAAAGTATGAAAAACACAGCGGGAATTGAAATT
*
1133847 AATTTAGAAGCTGAAAGGGAATTCAATATT-CTCATAGGATCTTCTTCTTTCTTAAT
66 AATTTAGAAGCTGAAAGGGAATTCAAT-TTCCTCATAGGATCTTCTTCTTCCTTAAT
1133903 GCATAGGATA
Statistics
Matches: 111, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
129 109 0.98
130 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (129 bp):
AGAGAGATAGAGAAGCTGCTCGGATAGCAGTGGAAAGTATGAAAAACACAGCGGGAATTGAAATT
AATTTAGAAGCTGAAAGGGAATTCAATTTCCTCATAGGATCTTCTTCTTCCTTAATCCATCGGA
Found at i:1134826 original size:32 final size:32
Alignment explanation
Indices: 1134790--1134875 Score: 84
Period size: 32 Copynumber: 2.7 Consensus size: 32
1134780 AGATCAGATT
*
1134790 TTTTCAGGTTAGGTCAATATCAAATCGATTAA
1 TTTTCAGGTTAGATCAATATCAAATCGATTAA
* * * * * *
1134822 TTTTCGGGTCATATTAATATCAAATCGTTTAG
1 TTTTCAGGTTAGATCAATATCAAATCGATTAA
*
1134854 TTTTCGGGTT-GAATCAATATCA
1 TTTTCAGGTTAG-ATCAATATCA
1134876 TATTGGTTGA
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (32 bp):
TTTTCAGGTTAGATCAATATCAAATCGATTAA
Found at i:1136049 original size:16 final size:16
Alignment explanation
Indices: 1136004--1136042 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1135994 TCGGTTTATA
*
1136004 TTTAGTTCGGGTTACT
1 TTTAGTTCGAGTTACT
*
1136020 TTCAGTTCGAGTTACT
1 TTTAGTTCGAGTTACT
1136036 TTTAGTT
1 TTTAGTT
1136043 TGTGTTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.21, T:0.51
Consensus pattern (16 bp):
TTTAGTTCGAGTTACT
Found at i:1137205 original size:129 final size:129
Alignment explanation
Indices: 1136973--1137222 Score: 421
Period size: 129 Copynumber: 1.9 Consensus size: 129
1136963 AAACAAAGGG
*
1136973 AGAGAGATAGAGAAGCTGCTCGGATCGCAGTGAAAAGTATGAAAAACACAGCTGGAATTGAAATT
1 AGAGAGATAGAGAAGCTGCTCGGATCGCAGTGAAAAGTATGAAAAACACAGCGGGAATTGAAATT
* *
1137038 AATTTAGATGCTGAAAGGGAATTCAATTTCCTCGTAGGATCTTCTTCTTCCTTAATCCATCGGA
66 AATTTAGAAGCTGAAAGGGAATTCAATTTCCTCATAGGATCTTCTTCTTCCTTAATCCATCGGA
* * * *
1137102 AGAGAGATAGAGAAGCTGCTCGGATGGCATTGGAAAGTATGAAAAACACAGCGGGGATTGAAATT
1 AGAGAGATAGAGAAGCTGCTCGGATCGCAGTGAAAAGTATGAAAAACACAGCGGGAATTGAAATT
1137167 AATTTAGAAGCTGAAAGGGAATTCAATATT-CTCATAGGATCTTCTTCTTCCTTAAT
66 AATTTAGAAGCTGAAAGGGAATTCAAT-TTCCTCATAGGATCTTCTTCTTCCTTAAT
1137223 GCATAGGATA
Statistics
Matches: 113, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
129 111 0.98
130 2 0.02
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (129 bp):
AGAGAGATAGAGAAGCTGCTCGGATCGCAGTGAAAAGTATGAAAAACACAGCGGGAATTGAAATT
AATTTAGAAGCTGAAAGGGAATTCAATTTCCTCATAGGATCTTCTTCTTCCTTAATCCATCGGA
Found at i:1138095 original size:17 final size:17
Alignment explanation
Indices: 1138073--1138108 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1138063 GTCGAGTCTA
1138073 GTCAATTTTCAGGTCGG
1 GTCAATTTTCAGGTCGG
*
1138090 GTCAATTTTCGGGTCGG
1 GTCAATTTTCAGGTCGG
1138107 GT
1 GT
1138109 GATAATTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.17, G:0.33, T:0.36
Consensus pattern (17 bp):
GTCAATTTTCAGGTCGG
Found at i:1139093 original size:21 final size:21
Alignment explanation
Indices: 1139078--1139133 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
1139068 AAGCAGAGAC
*
1139078 AGAAGCAAAGAGAGCATCGAG
1 AGAAGCAGAGAGAGCATCGAG
1139099 AGAAGCAGAGAGAGCATCGAG
1 AGAAGCAGAGAGAGCATCGAG
1139120 AGAAGCAGAGAGAG
1 AGAAGCAGAGAGAG
1139134 AAGCAACATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.46, C:0.12, G:0.38, T:0.04
Consensus pattern (21 bp):
AGAAGCAGAGAGAGCATCGAG
Found at i:1139111 original size:12 final size:11
Alignment explanation
Indices: 1139063--1139139 Score: 63
Period size: 12 Copynumber: 7.0 Consensus size: 11
1139053 AAGCTGAAGC
1139063 GAGAGAAGCAGA
1 GAGAGAAGCA-A
*
1139075 GACAGAAGCAA
1 GAGAGAAGCAA
*
1139086 -AGAG-AGCATC
1 GAGAGAAGCA-A
1139096 GAGAGAAGC-A
1 GAGAGAAGCAA
*
1139106 GAGAG-AGCATC
1 GAGAGAAGCA-A
1139117 GAGAGAAGCAGA
1 GAGAGAAGCA-A
1139129 GAGAGAAGCAA
1 GAGAGAAGCAA
1139140 CATTTTAGAA
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
9 7 0.13
10 8 0.15
11 11 0.21
12 26 0.50
ACGTcount: A:0.48, C:0.13, G:0.36, T:0.03
Consensus pattern (11 bp):
GAGAGAAGCAA
Found at i:1139582 original size:42 final size:41
Alignment explanation
Indices: 1139510--1139622 Score: 113
Period size: 42 Copynumber: 2.7 Consensus size: 41
1139500 GTTTCCCCCT
* *
1139510 AAAAACGCCGCTAAATGACCAACCTATTGCGGCAG-TTGTGCAC
1 AAAAACGCCGCTAAAT-ACAAACCTGTTGCGG-AGTTTGT-CAC
* * *
1139553 -GAAACGCCGCTAAATATCAAATCTGTTGCGGTGTTTGTCAC
1 AAAAACGCCGCTAAATA-CAAACCTGTTGCGGAGTTTGTCAC
1139594 TAAAAACGCCGCTAAATAGCAAACCTGTT
1 -AAAAACGCCGCTAAATA-CAAACCTGTT
1139623 ACGGGAAAAC
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
41 5 0.09
42 29 0.50
43 24 0.41
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (41 bp):
AAAAACGCCGCTAAATACAAACCTGTTGCGGAGTTTGTCAC
Found at i:1140329 original size:16 final size:15
Alignment explanation
Indices: 1140303--1140351 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
1140293 TTGGATCGGT
1140303 TTATATTTAGTTCGAG
1 TTAT-TTTAGTTCGAG
*
1140319 TTACTTTTAGTTTGAG
1 TTA-TTTTAGTTCGAG
*
1140335 TTATTTTCGGTTCGAG
1 TTATTTT-AGTTCGAG
1140351 T
1 T
1140352 CAAATTGTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 4 0.14
16 23 0.82
17 1 0.04
ACGTcount: A:0.18, C:0.08, G:0.20, T:0.53
Consensus pattern (15 bp):
TTATTTTAGTTCGAG
Found at i:1141138 original size:129 final size:129
Alignment explanation
Indices: 1140906--1141155 Score: 412
Period size: 129 Copynumber: 1.9 Consensus size: 129
1140896 AAACAACGGG
1140906 AGAGAGATAGAGAAACTGCTCGGACCGCATTGGAAAGCATGAAAAACACAGCAGGGATTGAAATT
1 AGAGAGATAGAGAAACTGCTCGGACCGCATTGGAAAGCATGAAAAACACAGCAGGGATTGAAATT
* *
1140971 AATTTAGATGCTGAAAGGGAATTCAATTTCCTCGTAGGATCTTCTTCTCCCTTAATCCATCGGA
66 AATTTAGAGGCTGAAAGGGAATTCAATTTCCTCATAGGATCTTCTTCTCCCTTAATCCATCGGA
** ** *
1141035 AGAGAGATAGAGAGGCTGCTCGGATGGCATTGGAAAGCATGAAAAACACAGCGGGGATTGAAATT
1 AGAGAGATAGAGAAACTGCTCGGACCGCATTGGAAAGCATGAAAAACACAGCAGGGATTGAAATT
*
1141100 AATTTAGAGGCTGAAAGGGAATTCAATATT-CTCATAGGATCTTCTTCTTCCTTAAT
66 AATTTAGAGGCTGAAAGGGAATTCAAT-TTCCTCATAGGATCTTCTTCTCCCTTAAT
1141156 GCATAGGATA
Statistics
Matches: 112, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
129 110 0.98
130 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (129 bp):
AGAGAGATAGAGAAACTGCTCGGACCGCATTGGAAAGCATGAAAAACACAGCAGGGATTGAAATT
AATTTAGAGGCTGAAAGGGAATTCAATTTCCTCATAGGATCTTCTTCTCCCTTAATCCATCGGA
Found at i:1142756 original size:6 final size:6
Alignment explanation
Indices: 1142710--1142755 Score: 83
Period size: 6 Copynumber: 7.7 Consensus size: 6
1142700 AGACACGTAT
*
1142710 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCCC GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC
1142756 CGTGCAGTGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.30, C:0.52, G:0.17, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:1144094 original size:21 final size:21
Alignment explanation
Indices: 1144065--1144113 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
1144055 AGCTGAAGCG
1144065 AGAGAAGCAGAGACAGAAGCAA
1 AGAG-AGCAGAGACAGAAGCAA
** * *
1144087 AGAGAGCATCGAGAGAAGCAG
1 AGAGAGCAGAGACAGAAGCAA
1144108 AGAGAG
1 AGAGAG
1144114 AAGCAACATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.49, C:0.12, G:0.37, T:0.02
Consensus pattern (21 bp):
AGAGAGCAGAGACAGAAGCAA
Found at i:1144112 original size:12 final size:12
Alignment explanation
Indices: 1144064--1144118 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
1144054 AAGCTGAAGC
1144064 GAGAGAAGCAGA
1 GAGAGAAGCAGA
*
1144076 GACAGAAGCA-A
1 GAGAGAAGCAGA
**
1144087 -AGAG-AGCATC
1 GAGAGAAGCAGA
1144097 GAGAGAAGCAGA
1 GAGAGAAGCAGA
1144109 GAGAGAAGCA
1 GAGAGAAGCA
1144119 ACATTTTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
9 4 0.11
10 3 0.09
11 5 0.14
12 23 0.66
ACGTcount: A:0.49, C:0.13, G:0.36, T:0.02
Consensus pattern (12 bp):
GAGAGAAGCAGA
Found at i:1145320 original size:16 final size:16
Alignment explanation
Indices: 1145296--1145343 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
1145286 GTTTATATTT
*
1145296 AGTTCGAGTTACTTTC
1 AGTTTGAGTTACTTTC
*
1145312 AGTTTGAGTTACTTTT
1 AGTTTGAGTTACTTTC
* *
1145328 AGTTTGTGTTATTTTC
1 AGTTTGAGTTACTTTC
1145344 GGTTCGAGTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.17, C:0.10, G:0.19, T:0.54
Consensus pattern (16 bp):
AGTTTGAGTTACTTTC
Found at i:1146524 original size:129 final size:129
Alignment explanation
Indices: 1146292--1146541 Score: 421
Period size: 129 Copynumber: 1.9 Consensus size: 129
1146282 AAACAAAGGG
*
1146292 AGAGAGATAGAGAAGCTGCTCGGATCGCAGTGGAAAGTATGAAAAACACAGCTGGAATTGAAATT
1 AGAGAGATAGAGAAGCTGCTCGGATCGCAGTGGAAAGTATGAAAAACACAGCGGGAATTGAAATT
* *
1146357 AATTTAGATGCTGAAAGGGAATTCAATTTCCTCGTAGGATCTTCTTCTTCCTTAATCCATCGGA
66 AATTTAGAAGCTGAAAGGGAATTCAATTTCCTCATAGGATCTTCTTCTTCCTTAATCCATCGGA
* * *
1146421 AGAGAGATAGAGAAGCTGCTCGGATGGCATTGGAAAGTATGAAAAACACAGCGGGGATTGAAATT
1 AGAGAGATAGAGAAGCTGCTCGGATCGCAGTGGAAAGTATGAAAAACACAGCGGGAATTGAAATT
*
1146486 AATTTAGAAGCTGAAAGGGAATTCAATATT-CTCATAGGATCTTCTTCTTTCTTAAT
66 AATTTAGAAGCTGAAAGGGAATTCAAT-TTCCTCATAGGATCTTCTTCTTCCTTAAT
1146542 GCATAGGATA
Statistics
Matches: 113, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
129 111 0.98
130 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (129 bp):
AGAGAGATAGAGAAGCTGCTCGGATCGCAGTGGAAAGTATGAAAAACACAGCGGGAATTGAAATT
AATTTAGAAGCTGAAAGGGAATTCAATTTCCTCATAGGATCTTCTTCTTCCTTAATCCATCGGA
Found at i:1147464 original size:32 final size:32
Alignment explanation
Indices: 1147428--1147513 Score: 84
Period size: 32 Copynumber: 2.7 Consensus size: 32
1147418 AGATCAGATT
*
1147428 TTTTCAGGTTAGGTCAATATCAAATCGATTAA
1 TTTTCAGGTTAGATCAATATCAAATCGATTAA
* * * * * *
1147460 TTTTCGGGTCATATTAATATCAAATCGTTTAG
1 TTTTCAGGTTAGATCAATATCAAATCGATTAA
*
1147492 TTTTCGGGTT-GAATCAATATCA
1 TTTTCAGGTTAG-ATCAATATCA
1147514 TATTGGTTGA
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (32 bp):
TTTTCAGGTTAGATCAATATCAAATCGATTAA
Found at i:1148689 original size:16 final size:16
Alignment explanation
Indices: 1148644--1148682 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1148634 TCGGTTTATA
*
1148644 TTTAGTTCGGGTTACT
1 TTTAGTTCGAGTTACT
*
1148660 TTCAGTTCGAGTTACT
1 TTTAGTTCGAGTTACT
1148676 TTTAGTT
1 TTTAGTT
1148683 TGTGTTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.21, T:0.51
Consensus pattern (16 bp):
TTTAGTTCGAGTTACT
Found at i:1150985 original size:13 final size:13
Alignment explanation
Indices: 1150940--1150994 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
1150930 CGGGATTTTA
1150940 ATTTTA-ATTATT
1 ATTTTATATTATT
1150952 -TTTTATATTACATT
1 ATTTTATATT--ATT
*
1150966 ATATTAT-TTATAT
1 ATTTTATATTAT-T
1150979 ATTTTATATTATT
1 ATTTTATATTATT
1150992 ATT
1 ATT
1150995 AGTTTTTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
11 5 0.14
12 5 0.14
13 11 0.31
14 9 0.26
15 5 0.14
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (13 bp):
ATTTTATATTATT
Found at i:1151325 original size:135 final size:136
Alignment explanation
Indices: 1151174--1151421 Score: 410
Period size: 137 Copynumber: 1.8 Consensus size: 136
1151164 ACATATTTTC
* *
1151174 TTTTTCTCCCTCTCATATTTAGCTA-T-TATATATATGGTGTTAATATTATTATATGTTTTTACT
1 TTTTTCTCCCTCTCATATTTAGCTATTATATATATATGGTATTAATATTATTATATGTTCTTACT
*
1151237 AACTTTATTTATTTTACTTTATACGCTATTATTTTACATTTTTTTATAATTTTTCTATTATTATT
66 AACTTTATTTATTCTACTTTATACGCTATTATTTTACATTTTTTTATAATTTTTCTATTATTATT
1151302 ATATAT
131 ATATAT
* * *
1151308 TTTTTCCTCCCTCTCATATTTAGCTATTATATATATATGGTATTGATATTCTTATATGTTCTTAT
1 TTTTT-CTCCCTCTCATATTTAGCTATTATATATATATGGTATTAATATTATTATATGTTCTTAC
*
1151373 TAATTTTATTTATTCTACTTTATACGCTATTATTTTACATTTTTTTATA
65 TAACTTTATTTATTCTACTTTATACGCTATTATTTTACATTTTTTTATA
1151422 TATGTACATA
Statistics
Matches: 104, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
134 5 0.05
135 20 0.19
136 1 0.01
137 78 0.75
ACGTcount: A:0.25, C:0.12, G:0.05, T:0.58
Consensus pattern (136 bp):
TTTTTCTCCCTCTCATATTTAGCTATTATATATATATGGTATTAATATTATTATATGTTCTTACT
AACTTTATTTATTCTACTTTATACGCTATTATTTTACATTTTTTTATAATTTTTCTATTATTATT
ATATAT
Found at i:1162142 original size:60 final size:62
Alignment explanation
Indices: 1162060--1162179 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 62
1162050 AATACTTCGC
* * *
1162060 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTGA-AAAA-AAAAAG-GAAAGAAAAGAACGT
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAGAAAAAGAGAAA-AAAAGAACGT
* *
1162120 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAGAAAAAGAGGAAAAAAGAAC
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAGAAAAAGAGAAAAAAAGAAC
1162180 AAAAGAAGAG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
60 31 0.60
61 4 0.08
62 14 0.27
63 3 0.06
ACGTcount: A:0.49, C:0.12, G:0.27, T:0.12
Consensus pattern (62 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAGAAAAAGAGAAAAAAAGAACGT
Found at i:1163401 original size:106 final size:104
Alignment explanation
Indices: 1162916--1163469 Score: 823
Period size: 105 Copynumber: 5.3 Consensus size: 104
1162906 TTTTACCCAT
*
1162916 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
1162981 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCCCA-ATTCAG
* * *
1163021 AGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATG
1 AGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
1163086 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCCCA-ATTCAG
* ** * * *
1163126 AGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCGAGACAATGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
1163191 AAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTC-CCAATTCAG
1163231 AGCCAATTTC-A----A-AACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
1163290 AAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGG
66 AAGGGACCGCTGGTTGTCAACAAAC-ATTTCCCAA-TTCAG
* **
1163331 AGCCAATTTCAACTTCATAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCAAAACG
1 AGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
1163396 AAGGGACTGCTGGTTGTCAACAAACAATTTCCCAATTTCGG
66 AAGGGACCGCTGGTTGTCAACAAAC-ATTTCCCAA-TTCAG
*
1163437 AGCCAATTTCAACTTCATAACGAAAGATATTGG
1 AGCCAATTTCAACTTCACAACGAAAGATATTGG
1163470 CCTCGAAACA
Statistics
Matches: 420, Mismatches: 20, Indels: 17
0.92 0.04 0.04
Matches are distributed among these distances:
99 70 0.17
100 20 0.05
101 1 0.00
104 1 0.00
105 208 0.50
106 120 0.29
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (104 bp):
AGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
AAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTCAG
Found at i:1164820 original size:13 final size:13
Alignment explanation
Indices: 1164775--1164829 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
1164765 CGGGATTTTA
1164775 ATTTTA-ATTATT
1 ATTTTATATTATT
1164787 -TTTTATATTACATT
1 ATTTTATATT--ATT
*
1164801 ATATTAT-TTATAT
1 ATTTTATATTAT-T
1164814 ATTTTATATTATT
1 ATTTTATATTATT
1164827 ATT
1 ATT
1164830 AGTTTTTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
11 5 0.14
12 5 0.14
13 11 0.31
14 9 0.26
15 5 0.14
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (13 bp):
ATTTTATATTATT
Found at i:1164978 original size:38 final size:37
Alignment explanation
Indices: 1164927--1165002 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 37
1164917 CATCTTGCAT
1164927 TTTATCCTATTATTT-CTTTACTTTTTT-TATTATTATA
1 TTTATCCTATTATTTACTTT--TTTTTTCTATTATTATA
* *
1164964 TTTATCTTCATTATTTAGTTTTTTTTTCTATTATTATA
1 TTTATCCT-ATTATTTACTTTTTTTTTCTATTATTATA
1165002 T
1 T
1165003 ACATATTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
37 13 0.38
38 18 0.53
39 3 0.09
ACGTcount: A:0.21, C:0.09, G:0.01, T:0.68
Consensus pattern (37 bp):
TTTATCCTATTATTTACTTTTTTTTTCTATTATTATA
Found at i:1165142 original size:144 final size:142
Alignment explanation
Indices: 1164986--1165267 Score: 467
Period size: 142 Copynumber: 2.0 Consensus size: 142
1164976 ATTTAGTTTT
* *
1164986 TTTTTCTATTATTA-TATACATATTTTTTTCCTCCCTCTCATATTTAGCTATTATATATATATGG
1 TTTTTCTATTATTATTATATATATATTTTTCCTCCCTCTCATATTTAGCTATTATATATATATGG
* * *
1165050 TGTTAATATTATTATATGTTTTTACTAACTTTATTTATTTTACTTTATACGCTATTATTTTACAT
66 TATTAATATTATTATATGTTCTTACTAACTTTATTTATTCTACTTTATACGCTATTATTTTACAT
*
1165115 TTTTTTTTATAA
131 TTTTTTATATAA
1165127 TTTTTCTATTATTATTATATATATATTTTTCCTCCCTCTCATATTTAGCTATTATATATATATGG
1 TTTTTCTATTATTATTATATATATATTTTTCCTCCCTCTCATATTTAGCTATTATATATATATGG
* * * *
1165192 TATTGATATTCTTATATGTTCTTATTAATTTTATTTATTCTACTTTATACGCTATTATTTTACAT
66 TATTAATATTATTATATGTTCTTACTAACTTTATTTATTCTACTTTATACGCTATTATTTTACAT
1165257 TTTTTTATATA
131 TTTTTTATATA
1165268 TGTACATATG
Statistics
Matches: 130, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
141 14 0.11
142 116 0.89
ACGTcount: A:0.26, C:0.11, G:0.04, T:0.58
Consensus pattern (142 bp):
TTTTTCTATTATTATTATATATATATTTTTCCTCCCTCTCATATTTAGCTATTATATATATATGG
TATTAATATTATTATATGTTCTTACTAACTTTATTTATTCTACTTTATACGCTATTATTTTACAT
TTTTTTATATAA
Found at i:1166823 original size:17 final size:17
Alignment explanation
Indices: 1166803--1166835 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1166793 GGGTCGAGTC
1166803 AATTTTCAGGTCGGGTT
1 AATTTTCAGGTCGGGTT
*
1166820 AATTTTCGGGTCGGGT
1 AATTTTCAGGTCGGGT
1166836 GATAATTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.12, G:0.33, T:0.39
Consensus pattern (17 bp):
AATTTTCAGGTCGGGTT
Found at i:1167882 original size:21 final size:21
Alignment explanation
Indices: 1167853--1167929 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
1167843 AGCTGAAGCG
*
1167853 AGAGAAGCAGAGACAGAAGCAA
1 AGAG-AGCAGAGAGAGAAGCAA
**
1167875 AGAGAGCATCGAGAGAAGCAA
1 AGAGAGCAGAGAGAGAAGCAA
** *
1167896 AGAGAGCATCGAGAGAAGCAG
1 AGAGAGCAGAGAGAGAAGCAA
1167917 AGAGAGC-GAGAGA
1 AGAGAGCAGAGAGA
1167930 AGCAGAGAGA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 4 0.08
21 41 0.84
22 4 0.08
ACGTcount: A:0.48, C:0.13, G:0.36, T:0.03
Consensus pattern (21 bp):
AGAGAGCAGAGAGAGAAGCAA
Found at i:1167921 original size:12 final size:12
Alignment explanation
Indices: 1167852--1167945 Score: 61
Period size: 12 Copynumber: 7.8 Consensus size: 12
1167842 AAGCTGAAGC
1167852 GAGAGAAGCAGA
1 GAGAGAAGCAGA
*
1167864 GACAGAAGCA-A
1 GAGAGAAGCAGA
**
1167875 -AGAG-AGCATC
1 GAGAGAAGCAGA
*
1167885 GAGAGAAGCAAA
1 GAGAGAAGCAGA
* *
1167897 GAGAGCATCGAGA
1 GAGAGAAGC-AGA
*
1167910 GAAGCAGAGAG-AGC
1 G-AG-AGA-AGCAGA
1167924 GAGAGAAGCAGA
1 GAGAGAAGCAGA
1167936 GAGAGAAGCA
1 GAGAGAAGCA
1167946 ACATTTTAGA
Statistics
Matches: 62, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
9 4 0.06
10 3 0.05
11 7 0.11
12 35 0.56
13 5 0.08
14 5 0.08
15 2 0.03
16 1 0.02
ACGTcount: A:0.48, C:0.13, G:0.37, T:0.02
Consensus pattern (12 bp):
GAGAGAAGCAGA
Found at i:1169143 original size:16 final size:16
Alignment explanation
Indices: 1169119--1169166 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
1169109 GTTTATATTT
*
1169119 AGTTCGAGTTACTTTC
1 AGTTTGAGTTACTTTC
*
1169135 AGTTTGAGTTACTTTT
1 AGTTTGAGTTACTTTC
* *
1169151 AGTTTGTGTTATTTTC
1 AGTTTGAGTTACTTTC
1169167 GGTTCGAGTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.17, C:0.10, G:0.19, T:0.54
Consensus pattern (16 bp):
AGTTTGAGTTACTTTC
Found at i:1170061 original size:129 final size:129
Alignment explanation
Indices: 1169829--1170078 Score: 412
Period size: 129 Copynumber: 1.9 Consensus size: 129
1169819 AAACAACGGG
1169829 AGAGAGATAGAGAAACTGCTCGGACCGCATTGGAAAGCATGAAAAACACAGCAGGGATTGAAATT
1 AGAGAGATAGAGAAACTGCTCGGACCGCATTGGAAAGCATGAAAAACACAGCAGGGATTGAAATT
* * *
1169894 AATTTAGATGCTGAAAGGGAATTCAATTTCCTCGTAGGATCTTCTTCTTCCTTAATCCATCGGA
66 AATTTAGAGGCTGAAAGGAAATTCAATTTCCTCATAGGATCTTCTTCTTCCTTAATCCATCGGA
* ** * *
1169958 AGAGAGATAGAGAAGCTGCTCGGATGGCATTGGAAAGTATGAAAAACACAGCGGGGATTGAAATT
1 AGAGAGATAGAGAAACTGCTCGGACCGCATTGGAAAGCATGAAAAACACAGCAGGGATTGAAATT
1170023 AATTTAGAGGCTGAAAGGAAATTCAATATT-CTCATAGGATCTTCTTCTTCCTTAAT
66 AATTTAGAGGCTGAAAGGAAATTCAAT-TTCCTCATAGGATCTTCTTCTTCCTTAAT
1170079 GCATAGGATA
Statistics
Matches: 112, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
129 110 0.98
130 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (129 bp):
AGAGAGATAGAGAAACTGCTCGGACCGCATTGGAAAGCATGAAAAACACAGCAGGGATTGAAATT
AATTTAGAGGCTGAAAGGAAATTCAATTTCCTCATAGGATCTTCTTCTTCCTTAATCCATCGGA
Found at i:1171048 original size:32 final size:32
Alignment explanation
Indices: 1170978--1171050 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
1170968 TCAGGTTAGG
*
1170978 TCAATATCAAATCGATTAATTTTCGGGTCATA
1 TCAATATCAAATAGATTAATTTTCGGGTCATA
* * * *
1171010 TTAATATCAAATAGTTTAGTTTTCGGGTTGA-A
1 TCAATATCAAATAGATTAATTTTCGGG-TCATA
1171042 TCAATATCA
1 TCAATATCA
1171051 TATCGGTTGA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 32 0.94
33 2 0.06
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (32 bp):
TCAATATCAAATAGATTAATTTTCGGGTCATA
Found at i:1172229 original size:16 final size:16
Alignment explanation
Indices: 1172184--1172222 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1172174 TCGGTTTATA
*
1172184 TTTAGTTCGGGTTACT
1 TTTAGTTCGAGTTACT
*
1172200 TTCAGTTCGAGTTACT
1 TTTAGTTCGAGTTACT
1172216 TTTAGTT
1 TTTAGTT
1172223 TGTGTTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.21, T:0.51
Consensus pattern (16 bp):
TTTAGTTCGAGTTACT
Found at i:1174523 original size:13 final size:13
Alignment explanation
Indices: 1174478--1174532 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
1174468 CGGGATTTTA
1174478 ATTTTA-ATTATT
1 ATTTTATATTATT
1174490 -TTTTATATTACATT
1 ATTTTATATT--ATT
*
1174504 ATATTAT-TTATAT
1 ATTTTATATTAT-T
1174517 ATTTTATATTATT
1 ATTTTATATTATT
1174530 ATT
1 ATT
1174533 AGTTTTTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
11 5 0.14
12 5 0.14
13 11 0.31
14 9 0.26
15 5 0.14
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (13 bp):
ATTTTATATTATT
Found at i:1174687 original size:18 final size:19
Alignment explanation
Indices: 1174663--1174710 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
1174653 TTACTTTTTT
1174663 TATTATTATATTTATCTTC
1 TATTATTATATTTATCTTC
* *
1174682 -ATTATT-TAGTTTTTTTTC
1 TATTATTATA-TTTATCTTC
1174700 TATTATTATAT
1 TATTATTATAT
1174711 ACATATTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
17 2 0.08
18 13 0.54
19 7 0.29
20 2 0.08
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (19 bp):
TATTATTATATTTATCTTC
Found at i:1174909 original size:140 final size:142
Alignment explanation
Indices: 1174694--1174974 Score: 458
Period size: 140 Copynumber: 2.0 Consensus size: 142
1174684 TATTTAGTTT
* *
1174694 TTTTTCTATTATTATATACATATTTTCTTTTTCTCCCTCTCATATTTAGCTATTATATATATATG
1 TTTTTCTATTATTATATACATATATTCTTTTCCTCCCTCTCATATTTAGCTATTATATATATATG
* * *
1174759 GTGTTAATATTATTATATGTTTTTACTAACTTTATTTATTTTACTTTATACGCTATTATTTTACA
66 GTATTAATATTATTATATGTTCTTACTAACTTTATTTATTCTACTTTATACGCTATTATTTTACA
1174824 TTTTTTTTATAA
131 TTTTTTTTATAA
*
1174836 TTTTTCTATTATTAT-TATATATATT-TTTTCCTCCCTCTCATATTTAGCTATTATATATATATG
1 TTTTTCTATTATTATATACATATATTCTTTTCCTCCCTCTCATATTTAGCTATTATATATATATG
* * * *
1174899 GTATTGATATTCTTATATGTTCTTATTAATTTTATTTATTCTACTTTATACGCTATTATTTTACA
66 GTATTAATATTATTATATGTTCTTACTAACTTTATTTATTCTACTTTATACGCTATTATTTTACA
1174964 TTTTTTTTATA
131 TTTTTTTTATA
1174975 TATGTACATA
Statistics
Matches: 129, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
140 106 0.82
141 8 0.06
142 15 0.12
ACGTcount: A:0.26, C:0.11, G:0.04, T:0.59
Consensus pattern (142 bp):
TTTTTCTATTATTATATACATATATTCTTTTCCTCCCTCTCATATTTAGCTATTATATATATATG
GTATTAATATTATTATATGTTCTTACTAACTTTATTTATTCTACTTTATACGCTATTATTTTACA
TTTTTTTTATAA
Found at i:1185696 original size:60 final size:62
Alignment explanation
Indices: 1185614--1185733 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 62
1185604 AATACTTCGC
* * *
1185614 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTGA-AAAA-AAAAAG-GAAAGAAAAGAACGT
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAGAAAAAGAGAAA-AAAAGAACGT
* *
1185674 TTAGGGTGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAGAAAAAGAGGAAAAAAGAAC
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAGAAAAAGAGAAAAAAAGAAC
1185734 AAAAGAAGAG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
60 31 0.60
61 4 0.08
62 14 0.27
63 3 0.06
ACGTcount: A:0.49, C:0.12, G:0.27, T:0.12
Consensus pattern (62 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTGAGAAAAGAAAAAGAGAAAAAAAGAACGT
Found at i:1186955 original size:106 final size:104
Alignment explanation
Indices: 1186470--1187023 Score: 823
Period size: 105 Copynumber: 5.3 Consensus size: 104
1186460 TTTTACCCAT
*
1186470 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
1186535 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCCCA-ATTCAG
* * *
1186575 AGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATG
1 AGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
1186640 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCCCA-ATTCAG
* ** * * *
1186680 AGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCGAGACAATGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
1186745 AAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTC-CCAATTCAG
1186785 AGCCAATTTC-A----A-AACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
1186844 AAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGG
66 AAGGGACCGCTGGTTGTCAACAAAC-ATTTCCCAA-TTCAG
* **
1186885 AGCCAATTTCAACTTCATAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCAAAACG
1 AGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
1186950 AAGGGACTGCTGGTTGTCAACAAACAATTTCCCAATTTCGG
66 AAGGGACCGCTGGTTGTCAACAAAC-ATTTCCCAA-TTCAG
*
1186991 AGCCAATTTCAACTTCATAACGAAAGATATTGG
1 AGCCAATTTCAACTTCACAACGAAAGATATTGG
1187024 CCTCGAAACA
Statistics
Matches: 420, Mismatches: 20, Indels: 17
0.92 0.04 0.04
Matches are distributed among these distances:
99 70 0.17
100 20 0.05
101 1 0.00
104 1 0.00
105 208 0.50
106 120 0.29
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (104 bp):
AGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
AAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTCAG
Found at i:1188358 original size:21 final size:20
Alignment explanation
Indices: 1188334--1188391 Score: 57
Period size: 21 Copynumber: 3.0 Consensus size: 20
1188324 TTTAATTTTA
1188334 ATTATTTTTATATTACATTAT
1 ATTATTTTTATATTACATT-T
* * *
1188355 ATTATTTATATTTTATA-TT
1 ATTATTTTTATATTACATTT
*
1188374 ATTAGTTTT-TATTACATT
1 ATTATTTTTATATTACATT
1188392 CGTATATATA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
18 5 0.17
19 9 0.31
20 1 0.03
21 14 0.48
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (20 bp):
ATTATTTTTATATTACATTT
Found at i:1188525 original size:18 final size:19
Alignment explanation
Indices: 1188501--1188548 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
1188491 TTACTTTTTT
1188501 TATTATTATATTTATCTTC
1 TATTATTATATTTATCTTC
* *
1188520 -ATTATT-TAGTTTTTTTTC
1 TATTATTATA-TTTATCTTC
1188538 TATTATTATAT
1 TATTATTATAT
1188549 ACATATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
17 2 0.08
18 13 0.54
19 7 0.29
20 2 0.08
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (19 bp):
TATTATTATATTTATCTTC
Found at i:1188716 original size:140 final size:142
Alignment explanation
Indices: 1188532--1188812 Score: 467
Period size: 140 Copynumber: 2.0 Consensus size: 142
1188522 TATTTAGTTT
*
1188532 TTTTTCTATTATTATATACATATTTTTTTTCCTCCCTCTCATATTTAGCTATTATATATATATGG
1 TTTTTCTATTATTATATACATATATTTTTTCCTCCCTCTCATATTTAGCTATTATATATATATGG
* * *
1188597 TGTTAATATTATTATATGTTTTTACTAACTTTATTTATTTTACTTTATACGCTATTATTTTACAT
66 TATTAATATTATTATATGTTCTTACTAACTTTATTTATTCTACTTTATACGCTATTATTTTACAT
1188662 TTTTTT-TATAA
131 TTTTTTATATAA
*
1188673 TTTTTCTATTATTAT-TATATATATTTTTTCCTCCCTCTCATATTTAGCTATTATATATATATGG
1 TTTTTCTATTATTATATACATATATTTTTTCCTCCCTCTCATATTTAGCTATTATATATATATGG
* * * *
1188737 TATTGATATTCTTATATGTTCTTATTAATTTTATTTATTCTACTTTATACGCTATTATTTTACAT
66 TATTAATATTATTATATGTTCTTACTAACTTTATTTATTCTACTTTATACGCTATTATTTTACAT
1188802 TTTTTTATATA
131 TTTTTTATATA
1188813 TGTACATATG
Statistics
Matches: 130, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
140 111 0.85
141 19 0.15
ACGTcount: A:0.26, C:0.11, G:0.04, T:0.58
Consensus pattern (142 bp):
TTTTTCTATTATTATATACATATATTTTTTCCTCCCTCTCATATTTAGCTATTATATATATATGG
TATTAATATTATTATATGTTCTTACTAACTTTATTTATTCTACTTTATACGCTATTATTTTACAT
TTTTTTATATAA
Found at i:1190369 original size:17 final size:17
Alignment explanation
Indices: 1190349--1190381 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1190339 GGGTCGAGTC
1190349 AATTTTCAGGTCGGGTT
1 AATTTTCAGGTCGGGTT
*
1190366 AATTTTCGGGTCGGGT
1 AATTTTCAGGTCGGGT
1190382 GATAATTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.12, G:0.33, T:0.39
Consensus pattern (17 bp):
AATTTTCAGGTCGGGTT
Found at i:1191428 original size:21 final size:21
Alignment explanation
Indices: 1191399--1191475 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
1191389 AGCTGAAGCG
*
1191399 AGAGAAGCAGAGACAGAAGCAA
1 AGAG-AGCAGAGAGAGAAGCAA
**
1191421 AGAGAGCATCGAGAGAAGCAA
1 AGAGAGCAGAGAGAGAAGCAA
** *
1191442 AGAGAGCATCGAGAGAAGCAG
1 AGAGAGCAGAGAGAGAAGCAA
1191463 AGAGAGC-GAGAGA
1 AGAGAGCAGAGAGA
1191476 AGCAGAGAGA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 4 0.08
21 41 0.84
22 4 0.08
ACGTcount: A:0.48, C:0.13, G:0.36, T:0.03
Consensus pattern (21 bp):
AGAGAGCAGAGAGAGAAGCAA
Found at i:1191467 original size:12 final size:12
Alignment explanation
Indices: 1191398--1191491 Score: 61
Period size: 12 Copynumber: 7.8 Consensus size: 12
1191388 AAGCTGAAGC
1191398 GAGAGAAGCAGA
1 GAGAGAAGCAGA
*
1191410 GACAGAAGCA-A
1 GAGAGAAGCAGA
**
1191421 -AGAG-AGCATC
1 GAGAGAAGCAGA
*
1191431 GAGAGAAGCAAA
1 GAGAGAAGCAGA
* *
1191443 GAGAGCATCGAGA
1 GAGAGAAGC-AGA
*
1191456 GAAGCAGAGAG-AGC
1 G-AG-AGA-AGCAGA
1191470 GAGAGAAGCAGA
1 GAGAGAAGCAGA
1191482 GAGAGAAGCA
1 GAGAGAAGCA
1191492 ACATTTTAGA
Statistics
Matches: 62, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
9 4 0.06
10 3 0.05
11 7 0.11
12 35 0.56
13 5 0.08
14 5 0.08
15 2 0.03
16 1 0.02
ACGTcount: A:0.48, C:0.13, G:0.37, T:0.02
Consensus pattern (12 bp):
GAGAGAAGCAGA
Found at i:1192687 original size:16 final size:16
Alignment explanation
Indices: 1192663--1192710 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
1192653 GTTTATATTT
*
1192663 AGTTCGAGTTACTTTC
1 AGTTTGAGTTACTTTC
*
1192679 AGTTTGAGTTACTTTT
1 AGTTTGAGTTACTTTC
* *
1192695 AGTTTGTGTTATTTTC
1 AGTTTGAGTTACTTTC
1192711 GGTTCGAGTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.17, C:0.10, G:0.19, T:0.54
Consensus pattern (16 bp):
AGTTTGAGTTACTTTC
Found at i:1193607 original size:129 final size:129
Alignment explanation
Indices: 1193375--1193624 Score: 412
Period size: 129 Copynumber: 1.9 Consensus size: 129
1193365 AAACAACGGG
1193375 AGAGAGATAGAGAAACTGCTCGGACCGCATTGGAAAGCATGAAAAACACAGCAGGGATTGAAATT
1 AGAGAGATAGAGAAACTGCTCGGACCGCATTGGAAAGCATGAAAAACACAGCAGGGATTGAAATT
* * *
1193440 AATTTAGATGCTGAAAGGGAATTCAATTTCCTCGTAGGATCTTCTTCTTCCTTAATCCATCGGA
66 AATTTAGAGGCTGAAAGGAAATTCAATTTCCTCATAGGATCTTCTTCTTCCTTAATCCATCGGA
* ** * *
1193504 AGAGAGATAGAGAAGCTGCTCGGATGGCATTGGAAAGTATGAAAAACACAGCGGGGATTGAAATT
1 AGAGAGATAGAGAAACTGCTCGGACCGCATTGGAAAGCATGAAAAACACAGCAGGGATTGAAATT
1193569 AATTTAGAGGCTGAAAGGAAATTCAATATT-CTCATAGGATCTTCTTCTTCCTTAAT
66 AATTTAGAGGCTGAAAGGAAATTCAAT-TTCCTCATAGGATCTTCTTCTTCCTTAAT
1193625 GCATAGGATA
Statistics
Matches: 112, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
129 110 0.98
130 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (129 bp):
AGAGAGATAGAGAAACTGCTCGGACCGCATTGGAAAGCATGAAAAACACAGCAGGGATTGAAATT
AATTTAGAGGCTGAAAGGAAATTCAATTTCCTCATAGGATCTTCTTCTTCCTTAATCCATCGGA
Done.