Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 182 of 206
Found at i:55527645 original size:50 final size:50
Alignment explanation
Indices: 55527586--55527689 Score: 181
Period size: 50 Copynumber: 2.1 Consensus size: 50
55527576 TTCTGGCACC
*
55527586 CAAGCAACATGCTTCGGAATTAGGCCTTATTTCTGTTGAAACTAAAAAGG
1 CAAGCAACATGCTTCCGAATTAGGCCTTATTTCTGTTGAAACTAAAAAGG
* *
55527636 CAAGCAACATGCTTCCGAATTAGGCCTTATTTCTGTTGGAACTAAGAAGG
1 CAAGCAACATGCTTCCGAATTAGGCCTTATTTCTGTTGAAACTAAAAAGG
55527686 CAAG
1 CAAG
55527690 TTAAGGACTA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (50 bp):
CAAGCAACATGCTTCCGAATTAGGCCTTATTTCTGTTGAAACTAAAAAGG
Found at i:55534818 original size:44 final size:44
Alignment explanation
Indices: 55534768--55535381 Score: 824
Period size: 44 Copynumber: 14.0 Consensus size: 44
55534758 GATCTGTTAC
* *
55534768 CTTCGATCTACTTCATGTCAATACATGGAGATAAGATCCAATAT
1 CTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCACTAT
**
55534812 CTTCGATCTACTTCATGTCAATACATGAAGATAAGATCTGCTAT
1 CTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCACTAT
* *
55534856 C-TCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTAT
1 CTTC-GATCTACTTCATGTCAATACATGAAGATAAGATCCACTAT
* *
55534900 CTTCGATCTACTTCATGTCAATACATGAAGATAAGATTCATTAT
1 CTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCACTAT
* **
55534944 CTTCGATCTACTTCACGTCAATACATGAAGATAAGATCTGCTAT
1 CTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCACTAT
* *
55534988 C-TCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTAT
1 CTTC-GATCTACTTCATGTCAATACATGAAGATAAGATCCACTAT
* *
55535032 CTTCGATCTACTCCATGTCAATACATGAAGATAAGATCCGCTAT
1 CTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCACTAT
* *
55535076 CTTTGATCTACTTCATGTCAATACATGAAGATAAGATCCATTAT
1 CTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCACTAT
* * * **
55535120 CCTCGATCTACTTCACGTCAATACATGAAGATAATATCTGCTAT
1 CTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCACTAT
* *
55535164 C-TCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTAT
1 CTTC-GATCTACTTCATGTCAATACATGAAGATAAGATCCACTAT
* **
55535208 CTTCGATCTACTCCATGTCAATACATGAAGATAAGATCTGCTAT
1 CTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCACTAT
* * *
55535252 C-TCTGATCTACTTAATGTCAATACATGAAGACAAGATCCATTAT
1 CTTC-GATCTACTTCATGTCAATACATGAAGATAAGATCCACTAT
* * ***
55535296 CTTTGATCTACTCCATGTCAATACATGAAGATAAGATTTGCTAT
1 CTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCACTAT
*
55535340 C-TCTGATCTACTTCATGTCAATACATGAAGACAAGATCCACT
1 CTTC-GATCTACTTCATGTCAATACATGAAGATAAGATCCACT
55535382 GCTTTTCAAC
Statistics
Matches: 495, Mismatches: 66, Indels: 18
0.85 0.11 0.03
Matches are distributed among these distances:
43 9 0.02
44 479 0.97
45 7 0.01
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (44 bp):
CTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCACTAT
Found at i:55534866 original size:88 final size:88
Alignment explanation
Indices: 55534751--55535379 Score: 940
Period size: 88 Copynumber: 7.1 Consensus size: 88
55534741 CCAGTATGGA
** * * ***
55534751 AAGACAAGATCTGTTACCTTCGATCTACTTCATGTCAATACATGGAGATAAGATCCAATATCT-T
1 AAGACAAGATCCATTATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCTGCTATCTCT
55534815 CGATCTACTTCATGTCAATACATG
66 -GATCTACTTCATGTCAATACATG
* *** * ***
55534839 AAGATAAGATCTGCTATC-TCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCT-
1 AAGACAAGATCCATTATCTTC-GATCTACTTCATGTCAATACATGAAGATAAGATCTGCTATCTC
55534902 TCGATCTACTTCATGTCAATACATG
65 T-GATCTACTTCATGTCAATACATG
* * *
55534927 AAGATAAGATTCATTATCTTCGATCTACTTCACGTCAATACATGAAGATAAGATCTGCTATCTCT
1 AAGACAAGATCCATTATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCTGCTATCTCT
55534992 GATCTACTTCATGTCAATACATG
66 GATCTACTTCATGTCAATACATG
* * *
55535015 AAGACAAGATCCATTATCTTCGATCTACTCCATGTCAATACATGAAGATAAGATCCGCTATCTTT
1 AAGACAAGATCCATTATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCTGCTATCTCT
55535080 GATCTACTTCATGTCAATACATG
66 GATCTACTTCATGTCAATACATG
* * * *
55535103 AAGATAAGATCCATTATCCTCGATCTACTTCACGTCAATACATGAAGATAATATCTGCTATCTCT
1 AAGACAAGATCCATTATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCTGCTATCTCT
55535168 GATCTACTTCATGTCAATACATG
66 GATCTACTTCATGTCAATACATG
*
55535191 AAGACAAGATCCATTATCTTCGATCTACTCCATGTCAATACATGAAGATAAGATCTGCTATCTCT
1 AAGACAAGATCCATTATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCTGCTATCTCT
*
55535256 GATCTACTTAATGTCAATACATG
66 GATCTACTTCATGTCAATACATG
* * *
55535279 AAGACAAGATCCATTATCTTTGATCTACTCCATGTCAATACATGAAGATAAGATTTGCTATCTCT
1 AAGACAAGATCCATTATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCTGCTATCTCT
55535344 GATCTACTTCATGTCAATACATG
66 GATCTACTTCATGTCAATACATG
55535367 AAGACAAGATCCA
1 AAGACAAGATCCA
55535380 CTGCTTTTCA
Statistics
Matches: 501, Mismatches: 37, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
87 2 0.00
88 496 0.99
89 3 0.01
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.32
Consensus pattern (88 bp):
AAGACAAGATCCATTATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCTGCTATCTCT
GATCTACTTCATGTCAATACATG
Found at i:55534988 original size:132 final size:132
Alignment explanation
Indices: 55534751--55535377 Score: 936
Period size: 132 Copynumber: 4.8 Consensus size: 132
55534741 CCAGTATGGA
** * * *
55534751 AAGACAAGATCTGTTACCTTCGATCTACTTCATGTCAATACATGGAGATAAGATCCAATATCTTC
1 AAGACAAGATCCATTATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCACTATCTTC
55534816 GATCTACTTCATGTCAATACATGAAGATAAGATCTGCTATCTCTGATCTACTTCATGTCAATACA
66 GATCTACTTCATGTCAATACATGAAGATAAGATCTGCTATCTCTGATCTACTTCATGTCAATACA
55534881 TG
131 TG
* *
55534883 AAGACAAGATCCATTATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATTCATTATCTTC
1 AAGACAAGATCCATTATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCACTATCTTC
*
55534948 GATCTACTTCACGTCAATACATGAAGATAAGATCTGCTATCTCTGATCTACTTCATGTCAATACA
66 GATCTACTTCATGTCAATACATGAAGATAAGATCTGCTATCTCTGATCTACTTCATGTCAATACA
55535013 TG
131 TG
* * *
55535015 AAGACAAGATCCATTATCTTCGATCTACTCCATGTCAATACATGAAGATAAGATCCGCTATCTTT
1 AAGACAAGATCCATTATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCACTATCTTC
*** *
55535080 GATCTACTTCATGTCAATACATGAAGATAAGATCCATTATC-CTCGATCTACTTCACGTCAATAC
66 GATCTACTTCATGTCAATACATGAAGATAAGATCTGCTATCTCT-GATCTACTTCATGTCAATAC
55535144 ATG
130 ATG
* * *** * *
55535147 AAGATAATATCTGCTATC-TCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTT
1 AAGACAAGATCCATTATCTTC-GATCTACTTCATGTCAATACATGAAGATAAGATCCACTATCTT
* *
55535211 CGATCTACTCCATGTCAATACATGAAGATAAGATCTGCTATCTCTGATCTACTTAATGTCAATAC
65 CGATCTACTTCATGTCAATACATGAAGATAAGATCTGCTATCTCTGATCTACTTCATGTCAATAC
55535276 ATG
130 ATG
* * ***
55535279 AAGACAAGATCCATTATCTTTGATCTACTCCATGTCAATACATGAAGATAAGATTTGCTATC-TC
1 AAGACAAGATCCATTATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCACTATCTTC
*
55535343 TGATCTACTTCATGTCAATACATGAAGACAAGATC
66 -GATCTACTTCATGTCAATACATGAAGATAAGATC
55535378 CACTGCTTTT
Statistics
Matches: 443, Mismatches: 47, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
131 6 0.01
132 434 0.98
133 3 0.01
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (132 bp):
AAGACAAGATCCATTATCTTCGATCTACTTCATGTCAATACATGAAGATAAGATCCACTATCTTC
GATCTACTTCATGTCAATACATGAAGATAAGATCTGCTATCTCTGATCTACTTCATGTCAATACA
TG
Found at i:55536654 original size:21 final size:21
Alignment explanation
Indices: 55536630--55536678 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
55536620 TTAGCCTCTC
*
55536630 CATTTTTACTTTTTCAT-TTTT
1 CATTTTT-CATTTTCATCTTTT
55536651 CATTTTTCATTTTCATCTTTT
1 CATTTTTCATTTTCATCTTTT
55536672 CATTTTT
1 CATTTTT
55536679 TCACATCACT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.69
Consensus pattern (21 bp):
CATTTTTCATTTTCATCTTTT
Found at i:55536681 original size:8 final size:7
Alignment explanation
Indices: 55536630--55536678 Score: 66
Period size: 7 Copynumber: 7.0 Consensus size: 7
55536620 TTAGCCTCTC
55536630 CATTTTT
1 CATTTTT
55536637 -ACTTTTT
1 CA-TTTTT
55536644 CATTTTT
1 CATTTTT
55536651 CATTTTT
1 CATTTTT
55536658 CA-TTTT
1 CATTTTT
55536664 CATCTTTT
1 CAT-TTTT
55536672 CATTTTT
1 CATTTTT
55536679 TCACATCACT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
6 7 0.18
7 23 0.61
8 8 0.21
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.69
Consensus pattern (7 bp):
CATTTTT
Found at i:55539606 original size:19 final size:20
Alignment explanation
Indices: 55539582--55539625 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
55539572 TACCAGTGTT
* *
55539582 TAATGCATATG-ATGTAATG
1 TAATGCAGATGCATGAAATG
55539601 TAATGCAGATGCATGAAATG
1 TAATGCAGATGCATGAAATG
55539621 -AATGC
1 TAATGC
55539626 CTAAAGAGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.30
Consensus pattern (20 bp):
TAATGCAGATGCATGAAATG
Found at i:55541447 original size:12 final size:13
Alignment explanation
Indices: 55541432--55541469 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
55541422 ATGCATATGC
55541432 ATATAT-TAAAAA
1 ATATATATAAAAA
*
55541444 ATATATATAAACAT
1 ATATATATAAA-AA
55541458 ATATATATAAAA
1 ATATATATAAAA
55541470 TGAATGAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 6 0.26
13 5 0.22
14 12 0.52
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (13 bp):
ATATATATAAAAA
Found at i:55541816 original size:3 final size:3
Alignment explanation
Indices: 55541803--55541858 Score: 51
Period size: 3 Copynumber: 18.3 Consensus size: 3
55541793 TTGTATGTAC
* * * *
55541803 ATA AAA ATA ATA ATT A-A ATA TTAA ATAA ATA ATA ATA ATA ATG ATA
1 ATA ATA ATA ATA ATA ATA ATA AT-A AT-A ATA ATA ATA ATA ATA ATA
55541849 ATA ATA ATA A
1 ATA ATA ATA A
55541859 GGAGAAAATA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 1 0.02
3 36 0.84
4 6 0.14
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:55544646 original size:15 final size:15
Alignment explanation
Indices: 55544622--55544651 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
55544612 AATGTTATTT
55544622 TTTAGAATTTTTTAA
1 TTTAGAATTTTTTAA
*
55544637 TTTAGTATTTTTTAA
1 TTTAGAATTTTTTAA
55544652 GAGTTATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (15 bp):
TTTAGAATTTTTTAA
Found at i:55545392 original size:22 final size:24
Alignment explanation
Indices: 55545361--55545419 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 24
55545351 TTAATATTAA
55545361 TATAAAAATTTTATTTA-AA-TTT
1 TATAAAAATTTTATTTATAATTTT
*
55545383 TATAACAA--TTATTTATAATTTT
1 TATAAAAATTTTATTTATAATTTT
*
55545405 TATAATACATTTTAT
1 TATAA-AAATTTTAT
55545420 ATTTTTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 7 0.24
21 2 0.07
22 15 0.52
23 1 0.03
25 4 0.14
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.54
Consensus pattern (24 bp):
TATAAAAATTTTATTTATAATTTT
Found at i:55549165 original size:27 final size:28
Alignment explanation
Indices: 55549134--55549192 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
55549124 TGACAAATCT
*
55549134 AATA-TTTTTTAATATG-TTTATAAAGGA
1 AATATTTTTTTAA-ATGTTTTATAAAGAA
*
55549161 AATATTTTTTTGAATGTTTTATAAAGAA
1 AATATTTTTTTAAATGTTTTATAAAGAA
55549189 AATA
1 AATA
55549193 ATTACTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.47
Consensus pattern (28 bp):
AATATTTTTTTAAATGTTTTATAAAGAA
Found at i:55549207 original size:28 final size:28
Alignment explanation
Indices: 55549134--55549208 Score: 68
Period size: 28 Copynumber: 2.7 Consensus size: 28
55549124 TGACAAATCT
* *
55549134 AATATT-TTTT-AATATGTTTATAAAGGA
1 AATATTCTTTTGAATGT-TTTATAAAGAA
*
55549161 AATATTTTTTTGAATGTTTTATAAAGAA
1 AATATTCTTTTGAATGTTTTATAAAGAA
55549189 AATAATTACTTTT-AA-GTTTT
1 AAT-ATT-CTTTTGAATGTTTT
55549209 TTCCTTCCGC
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
27 6 0.15
28 22 0.54
29 9 0.22
30 4 0.10
ACGTcount: A:0.39, C:0.01, G:0.09, T:0.51
Consensus pattern (28 bp):
AATATTCTTTTGAATGTTTTATAAAGAA
Found at i:55549969 original size:20 final size:20
Alignment explanation
Indices: 55549944--55549984 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
55549934 AAATGTGAAA
55549944 ACCTAAGATGTATACTTTCT
1 ACCTAAGATGTATACTTTCT
55549964 ACCTAAGATGTATACTTTCT
1 ACCTAAGATGTATACTTTCT
55549984 A
1 A
55549985 TCTTCCATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.39
Consensus pattern (20 bp):
ACCTAAGATGTATACTTTCT
Found at i:55551201 original size:40 final size:40
Alignment explanation
Indices: 55551120--55551311 Score: 271
Period size: 40 Copynumber: 4.8 Consensus size: 40
55551110 GGCCCATTTT
**
55551120 TATTTTAAAAAT-TTTTAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAAATATTTT-AAAATTAAAAAAA--ATTAAAAAAA
55551162 TATTTTAAAAATATTTTAAAATTAAAAAAAATTAAAAAAA
1 TATTTTAAAAATATTTTAAAATTAAAAAAAATTAAAAAAA
* *
55551202 TATTTTAAAAGTATTTTAAAATT-AAAAAAATTAAAAAAG
1 TATTTTAAAAATATTTTAAAATTAAAAAAAATTAAAAAAA
*
55551241 TATTTTAAAAATATTTTAAAATTTAAAAAAAATTAAAAAAG
1 TATTTTAAAAATATTTTAAAA-TTAAAAAAAATTAAAAAAA
* *
55551282 TATGTAAAAAATATTTTAAAATTAAAAAAA
1 TATTTTAAAAATATTTTAAAATTAAAAAAA
55551312 TAGATATATT
Statistics
Matches: 140, Mismatches: 7, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
39 35 0.25
40 41 0.29
41 35 0.25
42 25 0.18
43 4 0.03
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (40 bp):
TATTTTAAAAATATTTTAAAATTAAAAAAAATTAAAAAAA
Found at i:55551302 original size:11 final size:11
Alignment explanation
Indices: 55551120--55551261 Score: 94
Period size: 11 Copynumber: 13.9 Consensus size: 11
55551110 GGCCCATTTT
55551120 TATTTTAAAAA
1 TATTTTAAAAA
55551131 T-TTTT-AAAA
1 TATTTTAAAAA
**
55551140 -ATTAAAAAAA
1 TATTTTAAAAA
55551150 GTATTTTAAAAA
1 -TATTTTAAAAA
55551162 TATTTTAAAAA
1 TATTTTAAAAA
55551173 TATTTT--AAA
1 TATTTTAAAAA
*
55551182 -A-TTAAAAAA
1 TATTTTAAAAA
* **
55551191 AATTAAAAAAA
1 TATTTTAAAAA
*
55551202 TATTTTAAAAG
1 TATTTTAAAAA
55551213 TATTTT--AAA
1 TATTTTAAAAA
55551222 -A--TTAAAAA
1 TATTTTAAAAA
* *
55551230 -AATTAAAAAA
1 TATTTTAAAAA
55551240 GTATTTTAAAAA
1 -TATTTTAAAAA
55551252 TATTTTAAAA
1 TATTTTAAAA
55551262 TTTAAAAAAA
Statistics
Matches: 103, Mismatches: 14, Indels: 28
0.71 0.10 0.19
Matches are distributed among these distances:
6 2 0.02
7 2 0.02
8 6 0.06
9 14 0.14
10 15 0.15
11 48 0.47
12 16 0.16
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:55551640 original size:46 final size:46
Alignment explanation
Indices: 55551573--55551664 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
55551563 TTACGATTTG
*
55551573 GTCCCCACTTTTATATTTCAAATACATACCAAGAAATTTCTTATTA
1 GTCCCCACTTTTATATTTCAAATACAAACCAAGAAATTTCTTATTA
55551619 GTCCCCACTTTTATATTTCAAATACAAACCAAGAAATTTCTTATTA
1 GTCCCCACTTTTATATTTCAAATACAAACCAAGAAATTTCTTATTA
55551665 TTCCGATTTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.36, C:0.22, G:0.04, T:0.38
Consensus pattern (46 bp):
GTCCCCACTTTTATATTTCAAATACAAACCAAGAAATTTCTTATTA
Found at i:55551855 original size:2 final size:2
Alignment explanation
Indices: 55551850--55551892 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
55551840 TATACGTATT
55551850 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
55551892 T
1 T
55551893 CTAAATGCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55560477 original size:43 final size:45
Alignment explanation
Indices: 55560311--55560481 Score: 151
Period size: 44 Copynumber: 3.9 Consensus size: 45
55560301 GCATTACATG
* * *
55560311 ATTTCGTATAAGACCATAACTGGGCTA-TGGCATTGATATATG-A
1 ATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATATATGTA
* * * * *
55560354 GTCTTTGTGTAAGACCATATCT-GG-TATATAGCATCGATATATGTG
1 AT-TTCGTGTAAGACCATAGCTGGGCTAT-TGGCATCGATATATGTA
* * *
55560399 ATTACGTGTAAGACCAT-GTCTAGGAC-ATTGACATCG-T-TATGTA
1 ATTTCGTGTAAGACCATAG-CT-GGGCTATTGGCATCGATATATGTA
55560442 ATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATAT
1 ATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATAT
55560482 GTGATAACAT
Statistics
Matches: 98, Mismatches: 18, Indels: 22
0.71 0.13 0.16
Matches are distributed among these distances:
42 5 0.05
43 35 0.36
44 47 0.48
45 8 0.08
46 3 0.03
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (45 bp):
ATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATATATGTA
Found at i:55560495 original size:43 final size:43
Alignment explanation
Indices: 55560309--55560508 Score: 140
Period size: 43 Copynumber: 4.6 Consensus size: 43
55560299 TGGCATTACA
* * * * *
55560309 TGATTTCGTATAAGACCATAACTGGGCTA-TGGCATTGATATA
1 TGATTACGTGTAAGACCATAGCTGGGCTATTGGCATCGATATG
** * *
55560351 TGAGTCTTTGTGTAAGACCATATCT-GG-TATATAGCATCGATATATG
1 TGA-T-TACGTGTAAGACCATAGCTGGGCTAT-TGGCATCG--ATATG
* * *
55560397 TGATTACGTGTAAGACCAT-GTCTAGGAC-ATTGACATCGTTATG
1 TGATTACGTGTAAGACCATAG-CT-GGGCTATTGGCATCGATATG
* *
55560440 TAATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATATG
1 TGATTACGTGTAAGACCATAGCTGGGCTATTGGCATCGATATG
* * * *
55560483 TGATAACATGTAAGATCATATCTGGG
1 TGATTACGTGTAAGACCATAGCTGGG
55560509 ATATGACATT
Statistics
Matches: 122, Mismatches: 24, Indels: 23
0.72 0.14 0.14
Matches are distributed among these distances:
42 8 0.07
43 59 0.48
44 38 0.31
45 7 0.06
46 10 0.08
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (43 bp):
TGATTACGTGTAAGACCATAGCTGGGCTATTGGCATCGATATG
Found at i:55561857 original size:57 final size:57
Alignment explanation
Indices: 55561783--55561898 Score: 223
Period size: 57 Copynumber: 2.0 Consensus size: 57
55561773 GTTATTTTAC
*
55561783 TTAGAAAATTACTAAAGTTAGTTGAGTAAGTAGTGTATGGATTGGTTATACTTACAA
1 TTAGAAAATTACTAAAGTTAGTTGAGTAAGTAGTGTATGGATTAGTTATACTTACAA
55561840 TTAGAAAATTACTAAAGTTAGTTGAGTAAGTAGTGTATGGATTAGTTATACTTACAA
1 TTAGAAAATTACTAAAGTTAGTTGAGTAAGTAGTGTATGGATTAGTTATACTTACAA
55561897 TT
1 TT
55561899 GAGATTTGAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.38
Consensus pattern (57 bp):
TTAGAAAATTACTAAAGTTAGTTGAGTAAGTAGTGTATGGATTAGTTATACTTACAA
Found at i:55569619 original size:29 final size:29
Alignment explanation
Indices: 55569574--55569686 Score: 111
Period size: 29 Copynumber: 3.9 Consensus size: 29
55569564 GTGCTAGATG
* * *
55569574 ATGGTTGTAACCGTCCATTTTTATATTCA
1 ATGGTCGTAACCATCCATTTTCATATTCA
* * *
55569603 ATGGTCGAAACCATCCATTTTCATTAATCG
1 ATGGTCGTAACCATCCATTTTCA-TATTCA
* *
55569633 ATGGTCGTCACCATCCCTTTTCATAGTT-A
1 ATGGTCGTAACCATCCATTTTCATA-TTCA
* *
55569662 ATGGTCGTCACCATCCCTTTTCATA
1 ATGGTCGTAACCATCCATTTTCATA
55569687 ATCGATAGTC
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
29 46 0.65
30 25 0.35
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.38
Consensus pattern (29 bp):
ATGGTCGTAACCATCCATTTTCATATTCA
Found at i:55569639 original size:30 final size:29
Alignment explanation
Indices: 55569603--55569838 Score: 143
Period size: 29 Copynumber: 8.1 Consensus size: 29
55569593 TTTATATTCA
*
55569603 ATGGTCGAAACCATCCATTTTCATTAATCG
1 ATGGTCGAAACCATCCCTTTTCA-TAATCG
** * **
55569633 ATGGTCGTCACCATCCCTTTTCATAGTTA
1 ATGGTCGAAACCATCCCTTTTCATAATCG
**
55569662 ATGGTCGTCACCATCCCTTTTCATAATCG
1 ATGGTCGAAACCATCCCTTTTCATAATCG
* * * * *
55569691 ATAGTCGAAGCTAACCCTTTTCATATTCG
1 ATGGTCGAAACCATCCCTTTTCATAATCG
* * ** * *
55569720 ATAG-CCAAAGTTATCCCTTTTCATATTAG
1 ATGGTCGAAA-CCATCCCTTTTCATAATCG
*** * * *
55569749 ATAACCGAAGCTATCCCTTTTCATATTCG
1 ATGGTCGAAACCATCCCTTTTCATAATCG
* * *
55569778 ATGGTTGTAACCATCCTTTTTCATAATCG
1 ATGGTCGAAACCATCCCTTTTCATAATCG
* * * *
55569807 ATAG-CTGAAGCTATCCCTTTTCATATTCG
1 ATGGTC-GAAACCATCCCTTTTCATAATCG
55569836 ATG
1 ATG
55569839 ATCGCAGATA
Statistics
Matches: 160, Mismatches: 43, Indels: 7
0.76 0.20 0.03
Matches are distributed among these distances:
28 3 0.02
29 134 0.84
30 23 0.14
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (29 bp):
ATGGTCGAAACCATCCCTTTTCATAATCG
Found at i:55569737 original size:29 final size:29
Alignment explanation
Indices: 55569674--55569837 Score: 186
Period size: 29 Copynumber: 5.7 Consensus size: 29
55569664 GGTCGTCACC
* *
55569674 ATCCCTTTTCATAATCGATAGTCGAAGCT
1 ATCCCTTTTCATATTCGATAGCCGAAGCT
* * *
55569703 AACCCTTTTCATATTCGATAGCCAAAGTT
1 ATCCCTTTTCATATTCGATAGCCGAAGCT
* *
55569732 ATCCCTTTTCATATTAGATAACCGAAGCT
1 ATCCCTTTTCATATTCGATAGCCGAAGCT
* ** *
55569761 ATCCCTTTTCATATTCGATGGTTGTAA-CC
1 ATCCCTTTTCATATTCGATAGCCG-AAGCT
* * *
55569790 ATCCTTTTTCATAATCGATAGCTGAAGCT
1 ATCCCTTTTCATATTCGATAGCCGAAGCT
55569819 ATCCCTTTTCATATTCGAT
1 ATCCCTTTTCATATTCGAT
55569838 GATCGCAGAT
Statistics
Matches: 110, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
28 2 0.02
29 106 0.96
30 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.38
Consensus pattern (29 bp):
ATCCCTTTTCATATTCGATAGCCGAAGCT
Found at i:55569765 original size:87 final size:87
Alignment explanation
Indices: 55569674--55569833 Score: 214
Period size: 87 Copynumber: 1.8 Consensus size: 87
55569664 GGTCGTCACC
* * *
55569674 ATCCCTTTTCATAATCGATAGTCG-AAGCTAACCCTTTTCATATTCGATAGCCAAAGTTATCCCT
1 ATCCCTTTTCATAATCGATAGTCGTAA-CCAACCCTTTTCATAATCGATAGCCAAAGCTATCCCT
55569738 TTTCATATTAGATAACCGAAGCT
65 TTTCATATTAGATAACCGAAGCT
* * * * * **
55569761 ATCCCTTTTCATATTCGATGGTTGTAACCATCCTTTTTCATAATCGATAGCTGAAGCTATCCCTT
1 ATCCCTTTTCATAATCGATAGTCGTAACCAACCCTTTTCATAATCGATAGCCAAAGCTATCCCTT
55569826 TTCATATT
66 TTCATATT
55569834 CGATGATCGC
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
87 60 0.97
88 2 0.03
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.38
Consensus pattern (87 bp):
ATCCCTTTTCATAATCGATAGTCGTAACCAACCCTTTTCATAATCGATAGCCAAAGCTATCCCTT
TTCATATTAGATAACCGAAGCT
Found at i:55569838 original size:58 final size:58
Alignment explanation
Indices: 55569591--55569838 Score: 218
Period size: 58 Copynumber: 4.3 Consensus size: 58
55569581 TAACCGTCCA
* * * * * * *
55569591 TTTTTATATTCAATGGTCGAAACCATCCATTTTCATTAATCGAT-GGTCGTCA-CCATCCC
1 TTTTCATATTCGATGGTCGTAACCATCCCTTTTCA-TAATCGATAGCT-G-AAGCTATCCC
* * *
55569650 TTTTCATAGTT-AATGGTCGTCACCATCCCTTTTCATAATCGATAG-TCGAAGCTAACCC
1 TTTTCATA-TTCGATGGTCGTAACCATCCCTTTTCATAATCGATAGCT-GAAGCTATCCC
* ** ** * * * *
55569708 TTTTCATATTCGATAG-CCAAAGTTATCCCTTTTCATATTAGATAACCGAAGCTATCCC
1 TTTTCATATTCGATGGTCGTAA-CCATCCCTTTTCATAATCGATAGCTGAAGCTATCCC
* *
55569766 TTTTCATATTCGATGGTTGTAACCATCCTTTTTCATAATCGATAGCTGAAGCTATCCC
1 TTTTCATATTCGATGGTCGTAACCATCCCTTTTCATAATCGATAGCTGAAGCTATCCC
55569824 TTTTCATATTCGATG
1 TTTTCATATTCGATG
55569839 ATCGCAGATA
Statistics
Matches: 152, Mismatches: 30, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
57 5 0.03
58 114 0.75
59 31 0.20
60 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (58 bp):
TTTTCATATTCGATGGTCGTAACCATCCCTTTTCATAATCGATAGCTGAAGCTATCCC
Found at i:55578781 original size:64 final size:64
Alignment explanation
Indices: 55578680--55578808 Score: 258
Period size: 64 Copynumber: 2.0 Consensus size: 64
55578670 CTTTTGCAAA
55578680 TCGGCTGAACCACGCTCGTGGAGATTGTTTTAGCCCATACAAGGACTTCTTCAACTTACACACT
1 TCGGCTGAACCACGCTCGTGGAGATTGTTTTAGCCCATACAAGGACTTCTTCAACTTACACACT
55578744 TCGGCTGAACCACGCTCGTGGAGATTGTTTTAGCCCATACAAGGACTTCTTCAACTTACACACT
1 TCGGCTGAACCACGCTCGTGGAGATTGTTTTAGCCCATACAAGGACTTCTTCAACTTACACACT
55578808 T
1 T
55578809 GGTCCTTGTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.29
Consensus pattern (64 bp):
TCGGCTGAACCACGCTCGTGGAGATTGTTTTAGCCCATACAAGGACTTCTTCAACTTACACACT
Found at i:55584559 original size:2 final size:2
Alignment explanation
Indices: 55584552--55584579 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
55584542 AAACCTGCAT
55584552 GA GA 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
55584580 AAGGGGTAAT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:55592657 original size:16 final size:16
Alignment explanation
Indices: 55592619--55592657 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
55592609 TGGCAGTAGC
* *
55592619 AAAGAAAGCAAAAACG
1 AAAGAAAGAAAAAACA
*
55592635 AATGAAAGAAAAAACA
1 AAAGAAAGAAAAAACA
55592651 AAAGAAA
1 AAAGAAA
55592658 AGAACTCAGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.74, C:0.08, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAGAAAGAAAAAACA
Found at i:55598116 original size:13 final size:13
Alignment explanation
Indices: 55598100--55598125 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55598090 CTTTGCATAT
55598100 TGTCTTCAACAGG
1 TGTCTTCAACAGG
55598113 TGTCTTCAACAGG
1 TGTCTTCAACAGG
55598126 CTCGCACTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (13 bp):
TGTCTTCAACAGG
Found at i:55598379 original size:16 final size:16
Alignment explanation
Indices: 55598341--55598379 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
55598331 TGGCAGTAGC
* *
55598341 AAAGAAAGCAAAAACG
1 AAAGAAAGAAAAAACA
*
55598357 AATGAAAGAAAAAACA
1 AAAGAAAGAAAAAACA
55598373 AAAGAAA
1 AAAGAAA
55598380 AGAACTCAGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.74, C:0.08, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAGAAAGAAAAAACA
Found at i:55608532 original size:21 final size:21
Alignment explanation
Indices: 55608486--55608533 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
55608476 TTCCCATATT
55608486 TTTTTCTTTTATGTTCTTCTA
1 TTTTTCTTTTATGTTCTTCTA
* * *
55608507 ATTTTCTTTTTTTTTTCTT-TA
1 TTTTTC-TTTTATGTTCTTCTA
55608528 TTTTTC
1 TTTTTC
55608534 ATTCTCTTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.08, C:0.12, G:0.02, T:0.77
Consensus pattern (21 bp):
TTTTTCTTTTATGTTCTTCTA
Found at i:55612590 original size:21 final size:22
Alignment explanation
Indices: 55612546--55612590 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
55612536 GATATTTTAC
*
55612546 TATTTTTAAATTTAGGTATTGA
1 TATTTTTAAATTTAGGTATCGA
* *
55612568 TATTTTTACATTT-GGTGTCGA
1 TATTTTTAAATTTAGGTATCGA
55612589 TA
1 TA
55612591 CCTAATCATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.27, C:0.04, G:0.16, T:0.53
Consensus pattern (22 bp):
TATTTTTAAATTTAGGTATCGA
Found at i:55614828 original size:17 final size:19
Alignment explanation
Indices: 55614801--55614843 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
55614791 TAATTTAATA
55614801 ATAATTTAATTA-ATTTTT
1 ATAATTTAATTAGATTTTT
55614819 ATAA-TTAATTAGATTTTT
1 ATAATTTAATTAGATTTTT
*
55614837 ATTATTT
1 ATAATTT
55614844 TCAATTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 7 0.32
18 13 0.59
19 2 0.09
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
ATAATTTAATTAGATTTTT
Found at i:55615476 original size:2 final size:2
Alignment explanation
Indices: 55615431--55615460 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
55615421 AAACATTGTT
*
55615431 TA TA TT 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
55615461 AAAAATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:55616148 original size:36 final size:34
Alignment explanation
Indices: 55616089--55616190 Score: 107
Period size: 36 Copynumber: 2.9 Consensus size: 34
55616079 ATATAATTTT
* * *
55616089 TCAAATACATATGCCAAAAGCACATATTTATACTTA
1 TCAACTACATATGCCGAATGCACATA--TATACTTA
*
55616125 TCAACTACATGTGCCGAATGCACATATATACTTA
1 TCAACTACATATGCCGAATGCACATATATACTTA
*
55616159 T-AATCCACATATGCCGAATGCATACATATATA
1 TCAA-CTACATATGCCGAATGC--ACATATATA
55616191 TCCAAAAATT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
33 2 0.04
34 24 0.42
36 31 0.54
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (34 bp):
TCAACTACATATGCCGAATGCACATATATACTTA
Found at i:55616611 original size:41 final size:41
Alignment explanation
Indices: 55616369--55616602 Score: 351
Period size: 41 Copynumber: 5.7 Consensus size: 41
55616359 TTAATTTAAA
*
55616369 CAGATTCATCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* *
55616411 CAGATCATCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* *
55616452 CAAATCACCTGCACTTAGCCTGCTAGGCTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* *
55616493 CAGTTCACCTGCACTTAGCCTGCTAGGCTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* * *
55616534 CAGTTCACCGGCACTTAGCCTACTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* *
55616575 CAGATCATCGGCACTTAACCTGCTAGGC
1 CAGATCACCGGCACTTAGCCTGCTAGGC
55616603 GCTAAGCCTA
Statistics
Matches: 178, Mismatches: 14, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
41 174 0.98
42 4 0.02
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.29
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
Found at i:55617322 original size:2 final size:2
Alignment explanation
Indices: 55617260--55617306 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
55617250 ACACACACAC
55617260 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
55617302 TA TA T
1 TA TA T
55617307 TCGTACATTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55621107 original size:43 final size:43
Alignment explanation
Indices: 55621046--55621169 Score: 128
Period size: 43 Copynumber: 2.9 Consensus size: 43
55621036 ATTTTCGATA
* * *
55621046 TGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACT
1 TGTGTTTACGAGTAAGACCACGTCTGGGAAGTTGGCATCGACT
*
55621089 TGTGTTTACGAGTAAGACC-CTGTCTGGGATAG-TGGCATCGATT
1 TGTGTTTACGAGTAAGACCAC-GTCTGGGA-AGTTGGCATCGACT
** * *
55621132 TGTGAATAC-ATGTAAGACCACGTCTGGGATGTTTGCAT
1 TGTGTTTACGA-GTAAGACCACGTCTGGGAAGTTGGCAT
55621170 TGTACGAGCT
Statistics
Matches: 68, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
42 3 0.04
43 63 0.93
44 2 0.03
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTGTTTACGAGTAAGACCACGTCTGGGAAGTTGGCATCGACT
Found at i:55623876 original size:33 final size:33
Alignment explanation
Indices: 55623839--55623909 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
55623829 TGAACCAATT
*
55623839 AAAAAA-TCAATAAAATTGGCGGTTGAATCGACC
1 AAAAAACT-AATAAAACTGGCGGTTGAATCGACC
** * *
55623872 AAAAAACTAATTGAACTGGTGGTTGAATCGACT
1 AAAAAACTAATAAAACTGGCGGTTGAATCGACC
55623905 AAAAA
1 AAAAA
55623910 TGATTGAATC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.23
Consensus pattern (33 bp):
AAAAAACTAATAAAACTGGCGGTTGAATCGACC
Found at i:55625759 original size:21 final size:21
Alignment explanation
Indices: 55625711--55625764 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
55625701 ATAAAGTTGT
*
55625711 ATCTTTATAAGATAAAGATAC
1 ATCTTTATAACATAAAGATAC
**
55625732 AAATTTATGAACA-AAAGATAC
1 ATCTTTAT-AACATAAAGATAC
*
55625753 ATCTTTACAACA
1 ATCTTTATAACA
55625765 CAACTATTTG
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
20 4 0.15
21 19 0.73
22 3 0.12
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (21 bp):
ATCTTTATAACATAAAGATAC
Found at i:55628952 original size:18 final size:18
Alignment explanation
Indices: 55628931--55628973 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
55628921 GTTATAGTGC
55628931 TTTTAATCTATTTTTCTA
1 TTTTAATCTATTTTTCTA
** * *
55628949 TTTTAAAGTGTTTTTCTT
1 TTTTAATCTATTTTTCTA
55628967 TTTTAAT
1 TTTTAAT
55628974 TTTTTAATCT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.67
Consensus pattern (18 bp):
TTTTAATCTATTTTTCTA
Found at i:55635801 original size:13 final size:13
Alignment explanation
Indices: 55635783--55635807 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55635773 GCTCGATTGT
55635783 AATTATTTTTTAA
1 AATTATTTTTTAA
55635796 AATTATTTTTTA
1 AATTATTTTTTA
55635808 TATAAAAATA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
AATTATTTTTTAA
Found at i:55642327 original size:42 final size:42
Alignment explanation
Indices: 55642265--55642601 Score: 210
Period size: 42 Copynumber: 7.6 Consensus size: 42
55642255 GTTTACTTTT
* *
55642265 CGTTCAGCTTTTTTGAGCTTCTGTTTAACCCTTATGGGTTTC
1 CGTTCAGCTCTTTTGAGCTTCTGTTTAACCCTTATGAGTTTC
* * *
55642307 CGCTCAGCTCTTTTGAGCTTCTGTTTAACTCATATGAGTTTC
1 CGTTCAGCTCTTTTGAGCTTCTGTTTAACCCTTATGAGTTTC
* * *
55642349 TGTTCAGCTCTTTTGAGCTTTTGTTTAACCCTTATAAGTTTC
1 CGTTCAGCTCTTTTGAGCTTCTGTTTAACCCTTATGAGTTTC
* * * * *
55642391 CGTTCAGCTCTTATGAGCATATGAGTTTCTGTTCAGCTCTTTTGAGCTTT-
1 CGTTCAGCTC-T-T-----T-TGAGCTTCTGTTTAACCCTTATGAG-TTTC
* * * * * * * * *
55642441 TGTTTAACCCTTATAAGTTTCCGTTCAGCTCTTATGA-GCATATGAGTTTC
1 CGTTCAGCTCTTTTGAG----C-TTCTG-T-TTA--ACCCTTATGAGTTTC
* * *
55642491 TGTTCAGCTCTTTTGAGCTTTTGTTTAACCCTTATAAGTTTC
1 CGTTCAGCTCTTTTGAGCTTCTGTTTAACCCTTATGAGTTTC
* *
55642533 CGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGAGTTTC
1 CGTTCAGCTCTTTTGAGCTTCTGTTTAACCCTTATGAGTTTC
* * ** *
55642575 TGTTTAGCTCTCATGAACTTCTGTTTA
1 CGTTCAGCTCTTTTGAGCTTCTGTTTA
55642602 GCTTTCGAAC
Statistics
Matches: 223, Mismatches: 52, Indels: 40
0.71 0.17 0.13
Matches are distributed among these distances:
41 1 0.00
42 154 0.69
43 4 0.02
44 2 0.01
45 3 0.01
46 1 0.00
47 4 0.02
48 2 0.01
49 7 0.03
50 42 0.19
51 3 0.01
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.45
Consensus pattern (42 bp):
CGTTCAGCTCTTTTGAGCTTCTGTTTAACCCTTATGAGTTTC
Found at i:55642365 original size:21 final size:21
Alignment explanation
Indices: 55642262--55642407 Score: 89
Period size: 21 Copynumber: 7.0 Consensus size: 21
55642252 CATGTTTACT
* *
55642262 TTTC-GTTCAGCTTTTTTGAG
1 TTTCTGTTCAGCTCTTATGAG
* * * * *
55642282 CTTCTGTTTAACCCTTATGGG
1 TTTCTGTTCAGCTCTTATGAG
* * *
55642303 TTTCCGCTCAGCTCTTTTGAG
1 TTTCTGTTCAGCTCTTATGAG
* * * *
55642324 CTTCTGTTTAACTCATATGAG
1 TTTCTGTTCAGCTCTTATGAG
*
55642345 TTTCTGTTCAGCTCTTTTGAG
1 TTTCTGTTCAGCTCTTATGAG
* * * *
55642366 CTTT-TGTTTAACCCTTATAAG
1 -TTTCTGTTCAGCTCTTATGAG
*
55642387 TTTCCGTTCAGCTCTTATGAG
1 TTTCTGTTCAGCTCTTATGAG
55642408 CATATGAGTT
Statistics
Matches: 86, Mismatches: 37, Indels: 5
0.67 0.29 0.04
Matches are distributed among these distances:
20 6 0.07
21 77 0.90
22 3 0.03
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (21 bp):
TTTCTGTTCAGCTCTTATGAG
Found at i:55642453 original size:71 final size:71
Alignment explanation
Indices: 55642337--55642550 Score: 428
Period size: 71 Copynumber: 3.0 Consensus size: 71
55642327 CTGTTTAACT
55642337 CATATGAGTTTCTGTTCAGCTCTTTTGAGCTTTTGTTTAACCCTTATAAGTTTCCGTTCAGCTCT
1 CATATGAGTTTCTGTTCAGCTCTTTTGAGCTTTTGTTTAACCCTTATAAGTTTCCGTTCAGCTCT
55642402 TATGAG
66 TATGAG
55642408 CATATGAGTTTCTGTTCAGCTCTTTTGAGCTTTTGTTTAACCCTTATAAGTTTCCGTTCAGCTCT
1 CATATGAGTTTCTGTTCAGCTCTTTTGAGCTTTTGTTTAACCCTTATAAGTTTCCGTTCAGCTCT
55642473 TATGAG
66 TATGAG
55642479 CATATGAGTTTCTGTTCAGCTCTTTTGAGCTTTTGTTTAACCCTTATAAGTTTCCGTTCAGCTCT
1 CATATGAGTTTCTGTTCAGCTCTTTTGAGCTTTTGTTTAACCCTTATAAGTTTCCGTTCAGCTCT
55642544 TATGAG
66 TATGAG
55642550 C
1 C
55642551 TTCTGTTCAA
Statistics
Matches: 143, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 143 1.00
ACGTcount: A:0.18, C:0.20, G:0.17, T:0.45
Consensus pattern (71 bp):
CATATGAGTTTCTGTTCAGCTCTTTTGAGCTTTTGTTTAACCCTTATAAGTTTCCGTTCAGCTCT
TATGAG
Found at i:55642515 original size:21 final size:21
Alignment explanation
Indices: 55642481--55642604 Score: 106
Period size: 21 Copynumber: 5.9 Consensus size: 21
55642471 CTTATGAGCA
55642481 TATGAGTTTCTGTTCAGCTCT
1 TATGAGTTTCTGTTCAGCTCT
* * * *
55642502 TTTGAGCTTT-TGTTTAACCCT
1 TATGAG-TTTCTGTTCAGCTCT
* *
55642523 TATAAGTTTCCGTTCAGCTCT
1 TATGAGTTTCTGTTCAGCTCT
* * *
55642544 TATGAGCTTCTGTTCAACCCT
1 TATGAGTTTCTGTTCAGCTCT
*
55642565 TATGAGTTTCTGTTTAGCTCT
1 TATGAGTTTCTGTTCAGCTCT
* ** *
55642586 CATGAACTTCTGTTTAGCT
1 TATGAGTTTCTGTTCAGCT
55642605 TTCGAACTTC
Statistics
Matches: 79, Mismatches: 22, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
20 3 0.04
21 73 0.92
22 3 0.04
ACGTcount: A:0.17, C:0.21, G:0.16, T:0.46
Consensus pattern (21 bp):
TATGAGTTTCTGTTCAGCTCT
Found at i:55642613 original size:19 final size:20
Alignment explanation
Indices: 55642572--55642615 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
55642562 CCTTATGAGT
55642572 TTCTGTTTAGCTCTCATGAAC
1 TTCTGTTTAGCTCTCA-GAAC
*
55642593 TTCTGTTTAGCTTTC-GAAC
1 TTCTGTTTAGCTCTCAGAAC
55642612 TTCT
1 TTCT
55642616 ATCAACGATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.36
21 14 0.64
ACGTcount: A:0.16, C:0.23, G:0.14, T:0.48
Consensus pattern (20 bp):
TTCTGTTTAGCTCTCAGAAC
Found at i:55646713 original size:14 final size:14
Alignment explanation
Indices: 55646690--55646729 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
55646680 ACAGAAAAGT
*
55646690 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
55646704 AAATCATTTTACGG
1 AAAACATTTTACAG
55646718 AAAACATTTTAC
1 AAAACATTTTAC
55646730 TGGCTATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:55647325 original size:31 final size:30
Alignment explanation
Indices: 55647290--55647356 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 30
55647280 AAAAAAAACT
*
55647290 TAATATCTCAATGATTTAAATAAAAACTTTC
1 TAATAT-TCAACGATTTAAATAAAAACTTTC
* * *
55647321 TAATAATTTAGCGATTTAAATGAAAACTTTC
1 TAAT-ATTCAACGATTTAAATAAAAACTTTC
*
55647352 GAATA
1 TAATA
55647357 GTTTAATAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
30 1 0.03
31 27 0.90
32 2 0.07
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.37
Consensus pattern (30 bp):
TAATATTCAACGATTTAAATAAAAACTTTC
Found at i:55651697 original size:18 final size:19
Alignment explanation
Indices: 55651676--55651713 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
55651666 ATTTTGGCAT
*
55651676 TTTTATAAA-TAGTTTGAA
1 TTTTAAAAATTAGTTTGAA
*
55651694 TTTTAAAAATTATTTTGAA
1 TTTTAAAAATTAGTTTGAA
55651713 T
1 T
55651714 CTTTTTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (19 bp):
TTTTAAAAATTAGTTTGAA
Found at i:55664842 original size:63 final size:63
Alignment explanation
Indices: 55664750--55664919 Score: 223
Period size: 63 Copynumber: 2.7 Consensus size: 63
55664740 ATCACAACAC
** * * * *
55664750 GCACCAATTTATTTTACACTTGCACCACAACACGCGCAATCATTCATTGCACCAACATAGTCA
1 GCACCAATTTATTTTACACAAGCACCACAACATGCACAATCATTCACTGCACCAACACAGTCA
** * *
55664813 GCACCCTTTTATTTTACACAAGCATCACAACATGCACAATCATTCCCTGCACCAACACAGTCA
1 GCACCAATTTATTTTACACAAGCACCACAACATGCACAATCATTCACTGCACCAACACAGTCA
* * *
55664876 TCACCAATTTATTTTACACAAGCACCACAGCATGCTCAATCATT
1 GCACCAATTTATTTTACACAAGCACCACAACATGCACAATCATT
55664920 TCCTACACCG
Statistics
Matches: 91, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
63 91 1.00
ACGTcount: A:0.34, C:0.32, G:0.08, T:0.26
Consensus pattern (63 bp):
GCACCAATTTATTTTACACAAGCACCACAACATGCACAATCATTCACTGCACCAACACAGTCA
Found at i:55666725 original size:22 final size:21
Alignment explanation
Indices: 55666692--55666733 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
55666682 AAAACCAAAC
*
55666692 AAACAAATAAATAAAATAACG
1 AAACAAACAAATAAAATAACG
55666713 AAACTAAACAAATAAAATAAC
1 AAAC-AAACAAATAAAATAAC
55666734 AACCCAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.71, C:0.12, G:0.02, T:0.14
Consensus pattern (21 bp):
AAACAAACAAATAAAATAACG
Found at i:55668201 original size:20 final size:20
Alignment explanation
Indices: 55668171--55668216 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
55668161 TTAACATTAA
55668171 TAATAATTTTAAT-AGTATCTT
1 TAAT-ATTTTAATAAGTAT-TT
*
55668192 TAATATTTTATTAAGTATTT
1 TAATATTTTAATAAGTATTT
55668212 TAATA
1 TAATA
55668217 ATAAATACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.54
Consensus pattern (20 bp):
TAATATTTTAATAAGTATTT
Found at i:55669749 original size:31 final size:31
Alignment explanation
Indices: 55669710--55669778 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
55669700 TTACAATTTT
**
55669710 GTCACTAAACTATTTGAAAGTTTTCATTTAA
1 GTCACTAAACTATTCAAAAGTTTTCATTTAA
* *
55669741 GTTACTAAACTATTCAAAAGTTTTTATTTAA
1 GTCACTAAACTATTCAAAAGTTTTCATTTAA
55669772 GTCACTA
1 GTCACTA
55669779 GATTGTCAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (31 bp):
GTCACTAAACTATTCAAAAGTTTTCATTTAA
Found at i:55682718 original size:22 final size:22
Alignment explanation
Indices: 55682656--55682724 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
55682646 TATGCACTAT
* *
55682656 TAAACAAAGAGCACCAAA-ATGC
1 TAAACAGAGAGCA-CAAATGTGC
*
55682678 TATACAGAGAGCACAAATGTGC
1 TAAACAGAGAGCACAAATGTGC
* *
55682700 TAAACGGAGAGCACTAATGTGC
1 TAAACAGAGAGCACAAATGTGC
55682722 TAA
1 TAA
55682725 TAATAGGAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
21 4 0.10
22 36 0.90
ACGTcount: A:0.45, C:0.19, G:0.20, T:0.16
Consensus pattern (22 bp):
TAAACAGAGAGCACAAATGTGC
Found at i:55684682 original size:22 final size:23
Alignment explanation
Indices: 55684657--55684700 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
55684647 AATATAATAG
55684657 CAAAATGACAACAAA-ACAACAT
1 CAAAATGACAACAAACACAACAT
* * *
55684679 CAAAGTGGCAGCAAACACAACA
1 CAAAATGACAACAAACACAACA
55684701 GTAAACAGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.57, C:0.25, G:0.11, T:0.07
Consensus pattern (23 bp):
CAAAATGACAACAAACACAACAT
Found at i:55685174 original size:18 final size:17
Alignment explanation
Indices: 55685132--55685183 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 17
55685122 CGTAATTAAT
* *
55685132 AAATATATATAATATTGC
1 AAAT-TATATTATATTTC
55685150 AAA-TATATTATATTTC
1 AAATTATATTATATTTC
55685166 AAAATTATATTTATATTT
1 -AAATTATA-TTATATTT
55685184 TTTAATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 11 0.38
17 3 0.10
18 7 0.24
19 8 0.28
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (17 bp):
AAATTATATTATATTTC
Found at i:55697967 original size:93 final size:94
Alignment explanation
Indices: 55697808--55697993 Score: 293
Period size: 93 Copynumber: 2.0 Consensus size: 94
55697798 AAAAAGCAAG
* * * *
55697808 GCCATTGCAACACTAAAAAAGTAAAAACAAGGTAAAGTCCATAAAAACAAACATTGAAATCAAGG
1 GCCATTGCAACACTAAAAAAGTAAAAACAAGGCAAAGCCCATAAAAACAAACATGGAAAGCAAGG
55697873 GAATAAGTTG-AAAAAAGAAAGCAAGAAT
66 GAATAAGTTGAAAAAAAGAAAGCAAGAAT
* * * *
55697901 GCCATTGCAGCACTAAAGAAGTAAAAACGAGGCAAAGCCCATAAAAACAAATATGGAAAGCAAGG
1 GCCATTGCAACACTAAAAAAGTAAAAACAAGGCAAAGCCCATAAAAACAAACATGGAAAGCAAGG
55697966 GAATAAGTTGAAAAAAAGAAAGCAAGAA
66 GAATAAGTTGAAAAAAAGAAAGCAAGAA
55697994 AATCTAAAAC
Statistics
Matches: 84, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
93 67 0.80
94 17 0.20
ACGTcount: A:0.55, C:0.13, G:0.19, T:0.13
Consensus pattern (94 bp):
GCCATTGCAACACTAAAAAAGTAAAAACAAGGCAAAGCCCATAAAAACAAACATGGAAAGCAAGG
GAATAAGTTGAAAAAAAGAAAGCAAGAAT
Found at i:55698977 original size:25 final size:25
Alignment explanation
Indices: 55698946--55698995 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
55698936 ATACTCAGCC
55698946 AAAAAATGACTGAACCAAGGGTAAA
1 AAAAAATGACTGAACCAAGGGTAAA
**
55698971 AAAAAATGGTTGAACCAAGGGTAAA
1 AAAAAATGACTGAACCAAGGGTAAA
55698996 TAGATACCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.54, C:0.10, G:0.22, T:0.14
Consensus pattern (25 bp):
AAAAAATGACTGAACCAAGGGTAAA
Found at i:55703634 original size:21 final size:22
Alignment explanation
Indices: 55703610--55703653 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
55703600 AAAAAGTCAA
*
55703610 TAAATAAAAATTAT-TAAATAT
1 TAAATAAAAATCATATAAATAT
*
55703631 TAAATTAAAATCATATAAATAT
1 TAAATAAAAATCATATAAATAT
55703653 T
1 T
55703654 TTTTAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATAAAAATCATATAAATAT
Found at i:55705635 original size:48 final size:48
Alignment explanation
Indices: 55705582--55705677 Score: 156
Period size: 48 Copynumber: 2.0 Consensus size: 48
55705572 AAAAAAACCA
* * *
55705582 AAAAAATAAAGGGGGACTCATGACTGATGCTTGCTTCATAAGTGGTTC
1 AAAAAATAAAAGGGGACCCATGACCGATGCTTGCTTCATAAGTGGTTC
*
55705630 AAAAAATAAAAGGGGACCCATGACCGATGTTTGCTTCATAAGTGGTTC
1 AAAAAATAAAAGGGGACCCATGACCGATGCTTGCTTCATAAGTGGTTC
55705678 TTGTATTCTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (48 bp):
AAAAAATAAAAGGGGACCCATGACCGATGCTTGCTTCATAAGTGGTTC
Found at i:55707604 original size:73 final size:73
Alignment explanation
Indices: 55707527--55707689 Score: 175
Period size: 73 Copynumber: 2.2 Consensus size: 73
55707517 TGTATAACGA
* * * *
55707527 GAAGCTCATAAGAGCCATA-GTCAGAAAGCTCATGCGAGCCAATAACGGGTAGCTCCGAAGAGCC
1 GAAGCTCAAAAGAGCCATATATCAGAAAGCTCAAGCGAGCC-ATAACAGGTAGCTCCGAAGAGCC
55707591 ATTAATCGG
65 ATTAATCGG
*** * * * * * *
55707600 GAAGCTCCGGATAGCCATATATCGGGAAGTTCAAGTGAGCCATATCAGGTAGCTCCGAAGAGCCA
1 GAAGCTCAAAAGAGCCATATATCAGAAAGCTCAAGCGAGCCATAACAGGTAGCTCCGAAGAGCCA
55707665 TTAATCGG
66 TTAATCGG
*
55707673 GAAACTCACAAAGAGCC
1 GAAGCTCA-AAAGAGCC
55707690 TTTAATCGGG
Statistics
Matches: 71, Mismatches: 17, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
73 51 0.72
74 20 0.28
ACGTcount: A:0.34, C:0.23, G:0.26, T:0.17
Consensus pattern (73 bp):
GAAGCTCAAAAGAGCCATATATCAGAAAGCTCAAGCGAGCCATAACAGGTAGCTCCGAAGAGCCA
TTAATCGG
Found at i:55707605 original size:25 final size:25
Alignment explanation
Indices: 55707562--55707717 Score: 126
Period size: 25 Copynumber: 6.3 Consensus size: 25
55707552 AAGCTCATGC
* *
55707562 GAGCCAATAA-CGGGTAGCTCCGAA
1 GAGCCATTAATCGGGAAGCTCCGAA
*
55707586 GAGCCATTAATCGGGAAGCTCCGGA
1 GAGCCATTAATCGGGAAGCTCCGAA
* *
55707611 TAGCCA-TATATCGGGAAG-TTC-AA
1 GAGCCATTA-ATCGGGAAGCTCCGAA
* *
55707634 GTGAGCCA-T-ATCAGGTAGCTCCGAA
1 --GAGCCATTAATCGGGAAGCTCCGAA
* *
55707659 GAGCCATTAATCGGGAAACTCACAAA
1 GAGCCATTAATCGGGAAGCTC-CGAA
* *
55707685 GAGCCTTTAATCGGGAAGCTCATGAA
1 GAGCCATTAATCGGGAAGCTC-CGAA
55707711 GAGCCAT
1 GAGCCAT
55707718 ATAACAGGAC
Statistics
Matches: 104, Mismatches: 19, Indels: 16
0.75 0.14 0.12
Matches are distributed among these distances:
23 14 0.13
24 16 0.15
25 43 0.41
26 31 0.30
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (25 bp):
GAGCCATTAATCGGGAAGCTCCGAA
Found at i:55707694 original size:26 final size:26
Alignment explanation
Indices: 55707657--55707717 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
55707647 GGTAGCTCCG
55707657 AAGAGCCATTAATCGGGAAACTCACA
1 AAGAGCCATTAATCGGGAAACTCACA
* * **
55707683 AAGAGCCTTTAATCGGGAAGCTCATG
1 AAGAGCCATTAATCGGGAAACTCACA
55707709 AAGAGCCAT
1 AAGAGCCAT
55707718 ATAACAGGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (26 bp):
AAGAGCCATTAATCGGGAAACTCACA
Found at i:55712932 original size:21 final size:22
Alignment explanation
Indices: 55712873--55712934 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 22
55712863 CAGAAGCAGT
* * *
55712873 ATACAACACATAAAGTGCCTGA
1 ATACGACACATATAGTGCCTCA
** *
55712895 A-ACGACACACGTGGTGCC-CA
1 ATACGACACATATAGTGCCTCA
55712915 ATACGACACATATAGTGCCT
1 ATACGACACATATAGTGCCT
55712935 GATCGGCAAG
Statistics
Matches: 29, Mismatches: 9, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
20 2 0.07
21 26 0.90
22 1 0.03
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (22 bp):
ATACGACACATATAGTGCCTCA
Found at i:55714857 original size:24 final size:22
Alignment explanation
Indices: 55714830--55714873 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
55714820 ATTATTCCAC
55714830 CCTTAAAATATTTTCACTATTTGT
1 CCTTAAAAT-TTTTCA-TATTTGT
*
55714854 CCTTTAAATTTTTCATATTT
1 CCTTAAAATTTTTCATATTT
55714874 ACACTTTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 6 0.32
24 8 0.42
ACGTcount: A:0.27, C:0.16, G:0.02, T:0.55
Consensus pattern (22 bp):
CCTTAAAATTTTTCATATTTGT
Found at i:55715889 original size:27 final size:27
Alignment explanation
Indices: 55715851--55715905 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
55715841 ATAAAATACT
*
55715851 TAAAATGAAATGGGGTTCCTTTGAGAA
1 TAAAATGAAATGGGGTTCCTTTAAGAA
55715878 TAAAATGAAATGGGGTTCCTTTAAGAA
1 TAAAATGAAATGGGGTTCCTTTAAGAA
55715905 T
1 T
55715906 GAACTCGAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.07, G:0.24, T:0.31
Consensus pattern (27 bp):
TAAAATGAAATGGGGTTCCTTTAAGAA
Found at i:55716438 original size:4 final size:4
Alignment explanation
Indices: 55716429--55716572 Score: 168
Period size: 4 Copynumber: 39.0 Consensus size: 4
55716419 TTTAAGGGCA
55716429 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG
* * * *
55716477 -GAG AG-G AG-G AGAG -GAG GGAG GGAG GGAG GGAG -GAG -GAG -GAG
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG
55716518 -GAG AGAG AGAG AGAG AGAG -GAG -GAG AGAG AG-G AG-G AGAG AGAG
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG
55716561 AGAG AGAG AGAG
1 AGAG AGAG AGAG
55716573 TNNNNNNNNN
Statistics
Matches: 134, Mismatches: 0, Indels: 12
0.92 0.00 0.08
Matches are distributed among these distances:
3 36 0.27
4 98 0.73
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (4 bp):
AGAG
Found at i:55716487 original size:3 final size:3
Alignment explanation
Indices: 55716474--55716554 Score: 60
Period size: 3 Copynumber: 25.0 Consensus size: 3
55716464 GAGAGAGAGA
55716474 GAG GA- GAG GAG GA- GAG GAGG GAGG GAGG GAGG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GA-G GA-G GA-G GA-G GAG GAG GAG GAG GAG
55716521 AGAG AGAG AGAG AGAG GAG GA- GAG AGAG GAG GAG
1 -GAG -GAG -GAG -GAG GAG GAG GAG -GAG GAG GAG
55716555 AGAGAGAGAG
Statistics
Matches: 72, Mismatches: 0, Indels: 12
0.86 0.00 0.14
Matches are distributed among these distances:
2 6 0.08
3 33 0.46
4 33 0.46
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:55716681 original size:2 final size:2
Alignment explanation
Indices: 55716674--55716704 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
55716664 NNNNNNNNNN
55716674 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
55716705 CACAACTGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:55720418 original size:16 final size:16
Alignment explanation
Indices: 55720397--55720435 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
55720387 GTTTGGTTCA
*
55720397 CTGTAATGGAATAGAG
1 CTGTAATGGAATAAAG
55720413 CTGTAATGGAATAAAG
1 CTGTAATGGAATAAAG
55720429 CTGTAAT
1 CTGTAAT
55720436 CAGTAATTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.26, T:0.28
Consensus pattern (16 bp):
CTGTAATGGAATAAAG
Found at i:55722476 original size:21 final size:21
Alignment explanation
Indices: 55722435--55722476 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
55722425 TTCATATAAT
* *
55722435 AATTATATTAAGAATTTATTA
1 AATTATATTAACAATTAATTA
55722456 AATTATATTTAACAA-TAATTA
1 AATTATA-TTAACAATTAATTA
55722477 TGTTAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
AATTATATTAACAATTAATTA
Found at i:55722684 original size:49 final size:51
Alignment explanation
Indices: 55722618--55722716 Score: 125
Period size: 49 Copynumber: 2.0 Consensus size: 51
55722608 ATTACAACAT
*
55722618 CATTTCATTCAACCAAACACA-AGAA-TACT-ATTACAG-TTCTATTCCATTC
1 CATTCCATTCAACCAAACA-ATAGAATTACTGATTACAGCTT-TATTCCATTC
* *
55722667 CATTCCATTCAATCAAACAATTGAATTACTGATTACAGCTTTATTCCATT
1 CATTCCATTCAACCAAACAATAGAATTACTGATTACAGCTTTATTCCATT
55722717 ACAGCTCTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
48 1 0.02
49 20 0.47
50 4 0.09
51 16 0.37
52 2 0.05
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.35
Consensus pattern (51 bp):
CATTCCATTCAACCAAACAATAGAATTACTGATTACAGCTTTATTCCATTC
Found at i:55722719 original size:16 final size:16
Alignment explanation
Indices: 55722698--55722733 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
55722688 TGAATTACTG
* *
55722698 ATTACAGCTTTATTCC
1 ATTACAGCTCTATTCA
55722714 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCA
55722730 ATTA
1 ATTA
55722734 TAGTTAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTACAGCTCTATTCA
Found at i:55723774 original size:23 final size:22
Alignment explanation
Indices: 55723712--55723778 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
55723702 AGGTATCTAC
*
55723712 AAATCAAATCTCTAAGATTACA
1 AAATCATATCTCTAAGATTACA
55723734 AAATCATATCTCTAAGATTACA
1 AAATCATATCTCTAAGATTACA
55723756 AAATCATATCTTCTAAGATTACA
1 AAATCATATC-TCTAAGATTACA
55723779 TATTATATCT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.46, C:0.18, G:0.04, T:0.31
Consensus pattern (22 bp):
AAATCATATCTCTAAGATTACA
Found at i:55730027 original size:5 final size:5
Alignment explanation
Indices: 55730017--55730068 Score: 51
Period size: 5 Copynumber: 11.0 Consensus size: 5
55730007 TTTGACCTCC
55730017 TTAAA TTAAA TT--A TTAAA TTAAAA TT--A TTAAA -TAAA TTAAA TTAAAA
1 TTAAA TTAAA TTAAA TTAAA TT-AAA TTAAA TTAAA TTAAA TTAAA TT-AAA
55730064 TTAAA
1 TTAAA
55730069 GAATTAAAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
3 6 0.15
4 4 0.10
5 20 0.50
6 10 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TTAAA
Found at i:55730043 original size:14 final size:13
Alignment explanation
Indices: 55730017--55730055 Score: 62
Period size: 14 Copynumber: 3.0 Consensus size: 13
55730007 TTTGACCTCC
55730017 TTAAATTAAATTA
1 TTAAATTAAATTA
55730030 TTAAATTAAAATTA
1 TTAAATT-AAATTA
55730044 TTAAA-TAAATTA
1 TTAAATTAAATTA
55730056 AATTAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 6 0.24
13 8 0.32
14 11 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAATTAAATTA
Found at i:55730058 original size:23 final size:22
Alignment explanation
Indices: 55730021--55730066 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
55730011 ACCTCCTTAA
*
55730021 ATTAAATTATTAAATTAAAATT
1 ATTAAATAATTAAATTAAAATT
55730043 ATTAAATAAATTAAATTAAAATT
1 ATTAAAT-AATTAAATTAAAATT
55730066 A
1 A
55730067 AAGAATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTAAATAATTAAATTAAAATT
Found at i:55731749 original size:26 final size:26
Alignment explanation
Indices: 55731720--55731777 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
55731710 CCTGTTATAT
55731720 GGCTCTTCATGAGCTTCCTAATTAAA
1 GGCTCTTCATGAGCTTCCTAATTAAA
** * *
55731746 GGCTCTTTGTGAGCTTCCTGATTAAT
1 GGCTCTTCATGAGCTTCCTAATTAAA
55731772 GGCTCT
1 GGCTCT
55731778 CCGGAGCTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (26 bp):
GGCTCTTCATGAGCTTCCTAATTAAA
Found at i:55737597 original size:25 final size:25
Alignment explanation
Indices: 55737569--55737633 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
55737559 CTGTCTTTGA
*
55737569 TAGTATATCCTGAAACTACTATAGG
1 TAGTATATACTGAAACTACTATAGG
* *
55737594 TAGTATATACTGAGACTACTATAGA
1 TAGTATATACTGAAACTACTATAGG
55737619 TAG-ACTATACTGAAA
1 TAGTA-TATACTGAAA
55737634 ACACTTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 1 0.03
25 34 0.97
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (25 bp):
TAGTATATACTGAAACTACTATAGG
Found at i:55743614 original size:18 final size:18
Alignment explanation
Indices: 55743593--55743637 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
55743583 ACAATTAAAA
55743593 AACGTTTTG-AAATTGAAT
1 AACGTTTTGTAAA-TGAAT
*
55743611 AACGATTTGTAAATGAAT
1 AACGTTTTGTAAATGAAT
*
55743629 AATGTTTTG
1 AACGTTTTG
55743638 GAAACAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (18 bp):
AACGTTTTGTAAATGAAT
Found at i:55744745 original size:24 final size:25
Alignment explanation
Indices: 55744721--55744803 Score: 78
Period size: 25 Copynumber: 3.3 Consensus size: 25
55744711 GCATGTAAAC
55744721 GGAAGCTCTTTCGAGCCATATAACG
1 GGAAGCTCTTTCGAGCCATATAACG
* * **
55744746 GGAAACTCATGT-GAGCTGTATAACG
1 GGAAGCTC-TTTCGAGCCATATAACG
* * **
55744771 GGAAGCTCTTACGAGCCATTTATTG
1 GGAAGCTCTTTCGAGCCATATAACG
55744796 GGAAGCTC
1 GGAAGCTC
55744804 AAGAGAACCA
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
24 1 0.02
25 41 0.93
26 2 0.05
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (25 bp):
GGAAGCTCTTTCGAGCCATATAACG
Found at i:55744786 original size:25 final size:25
Alignment explanation
Indices: 55744696--55744786 Score: 78
Period size: 25 Copynumber: 3.6 Consensus size: 25
55744686 TTCATATTCA
55744696 GGAATGCTCATACGAGCATGTA-AAC-
1 GGAA-GCTCATACGAGC-TGTATAACG
* * **
55744721 GGAAGCTCTTTCGAGCCATATAACG
1 GGAAGCTCATACGAGCTGTATAACG
* **
55744746 GGAAACTCATGTGAGCTGTATAACG
1 GGAAGCTCATACGAGCTGTATAACG
*
55744771 GGAAGCTCTTACGAGC
1 GGAAGCTCATACGAGC
55744787 CATTTATTGG
Statistics
Matches: 50, Mismatches: 14, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
23 2 0.04
24 13 0.26
25 35 0.70
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.22
Consensus pattern (25 bp):
GGAAGCTCATACGAGCTGTATAACG
Found at i:55746770 original size:10 final size:11
Alignment explanation
Indices: 55746749--55746777 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
55746739 TTTCTTATTT
55746749 CTATTCTTTAG
1 CTATTCTTTAG
55746760 CTATT-TTTAG
1 CTATTCTTTAG
55746770 CTATTCTT
1 CTATTCTT
55746778 CTCACCTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.17, C:0.17, G:0.07, T:0.59
Consensus pattern (11 bp):
CTATTCTTTAG
Found at i:55749041 original size:21 final size:22
Alignment explanation
Indices: 55749017--55749057 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
55749007 AACGCTTATG
55749017 AAAAG-ATCACTTGGATTTAAA
1 AAAAGTATCACTTGGATTTAAA
* *
55749038 AAAAGTGTCGCTTGGATTTA
1 AAAAGTATCACTTGGATTTA
55749058 TCCATAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.32
Consensus pattern (22 bp):
AAAAGTATCACTTGGATTTAAA
Found at i:55749204 original size:13 final size:13
Alignment explanation
Indices: 55749186--55749210 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55749176 ATTATTTATC
55749186 ATTTAAATATATA
1 ATTTAAATATATA
55749199 ATTTAAATATAT
1 ATTTAAATATAT
55749211 TAATAATATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTAAATATATA
Found at i:55749218 original size:24 final size:22
Alignment explanation
Indices: 55749189--55749245 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
55749179 ATTTATCATT
*
55749189 TAAATATATAATTTAAATATATTAA
1 TAAATATATAA--T-AATATATAAA
*
55749214 T-AATATAGAATAATATATAAA
1 TAAATATATAATAATATATAAA
55749235 TAAATATATAA
1 TAAATATATAA
55749246 AGAAAATATG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 10 0.36
22 9 0.32
24 8 0.29
25 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
TAAATATATAATAATATATAAA
Found at i:55749241 original size:10 final size:11
Alignment explanation
Indices: 55749189--55749245 Score: 55
Period size: 11 Copynumber: 5.0 Consensus size: 11
55749179 ATTTATCATT
55749189 TAAATATATAA
1 TAAATATATAA
55749200 TTTAAATATATTAA
1 --TAAATATA-TAA
*
55749214 T-AATATAGAA
1 TAAATATATAA
55749224 T-AATATATAAA
1 TAAATATAT-AA
55749235 TAAATATATAA
1 TAAATATATAA
55749246 AGAAAATATG
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
10 9 0.23
11 11 0.28
12 8 0.21
13 8 0.21
14 3 0.08
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
TAAATATATAA
Found at i:55752610 original size:6 final size:5
Alignment explanation
Indices: 55752576--55752609 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
55752566 AAAATCTAGG
55752576 TTTTC -TTTC TTTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC -TTTTC TTTTC TTTTC TTTTC TTTT
55752610 TTCTGCTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 19 0.70
6 4 0.15
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:55753494 original size:3 final size:3
Alignment explanation
Indices: 55753486--55753511 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
55753476 TAGGTTTTCT
55753486 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
55753512 GTGAAATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:55767590 original size:15 final size:15
Alignment explanation
Indices: 55767554--55767582 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
55767544 AAAAAGAAAT
55767554 AGAAAAACGAAGCAA
1 AGAAAAACGAAGCAA
55767569 AGAAAAACGAAGCA
1 AGAAAAACGAAGCA
55767583 GAAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.66, C:0.14, G:0.21, T:0.00
Consensus pattern (15 bp):
AGAAAAACGAAGCAA
Found at i:55767590 original size:16 final size:15
Alignment explanation
Indices: 55767556--55767591 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
55767546 AAAGAAATAG
*
55767556 AAAAACGAAGCAAAG
1 AAAAACGAAGCAAAA
55767571 AAAAACGAAGCAGAAA
1 AAAAACGAAGCA-AAA
55767587 AAAAA
1 AAAAA
55767592 AAGAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.72, C:0.11, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAACGAAGCAAAA
Found at i:55768687 original size:12 final size:14
Alignment explanation
Indices: 55768670--55768702 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
55768660 AATGGGACAG
55768670 TGAATTGA-A-ATA
1 TGAATTGAGACATA
55768682 TGAATTGAGACATA
1 TGAATTGAGACATA
55768696 TGAATTG
1 TGAATTG
55768703 TGTATTCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
13 1 0.05
14 10 0.53
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.33
Consensus pattern (14 bp):
TGAATTGAGACATA
Found at i:55772712 original size:62 final size:62
Alignment explanation
Indices: 55772630--55772755 Score: 216
Period size: 62 Copynumber: 2.0 Consensus size: 62
55772620 AGGTGTTACA
*
55772630 TCTATTCTACTATTTTAACATTGATTGACCTTTATGTAGGTTGCCTCTTTCAGTTACCTCTT
1 TCTATTCTACTATTTTAACATTGATTGACCTTTATGTAGATTGCCTCTTTCAGTTACCTCTT
* * *
55772692 TCTATTTTACTCTTTTAACATTGATTGACCTTTATGTAGATTGCCTCTTTTAGTTACCTCTT
1 TCTATTCTACTATTTTAACATTGATTGACCTTTATGTAGATTGCCTCTTTCAGTTACCTCTT
55772754 TC
1 TC
55772756 CTTACCATCT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.19, C:0.21, G:0.10, T:0.50
Consensus pattern (62 bp):
TCTATTCTACTATTTTAACATTGATTGACCTTTATGTAGATTGCCTCTTTCAGTTACCTCTT
Found at i:55775105 original size:36 final size:36
Alignment explanation
Indices: 55775064--55775208 Score: 254
Period size: 36 Copynumber: 4.0 Consensus size: 36
55775054 GGTAGCATTA
55775064 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
55775100 GCTACACTTATCTGATCAAGTGAGAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
55775136 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
55775172 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
55775208 G
1 G
55775209 GTAGCCTTAG
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 105 1.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:55775156 original size:21 final size:20
Alignment explanation
Indices: 55775128--55775193 Score: 52
Period size: 21 Copynumber: 3.5 Consensus size: 20
55775118 AGTGAGAAAG
55775128 TGATAAGTGCTATACTTATC
1 TGATAAGTGCTATACTTATC
* **
55775148 TGATCAAGTG--A-A--AAAG
1 TGAT-AAGTGCTATACTTATC
55775164 TGATAAGTGCTATACTTATC
1 TGATAAGTGCTATACTTATC
55775184 TGATCAAGTG
1 TGAT-AAGTG
55775194 ACAAAGTGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 13
0.63 0.12 0.25
Matches are distributed among these distances:
15 5 0.15
16 5 0.15
17 1 0.03
18 2 0.06
19 1 0.03
20 9 0.27
21 10 0.30
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (20 bp):
TGATAAGTGCTATACTTATC
Found at i:55785841 original size:19 final size:20
Alignment explanation
Indices: 55785810--55785857 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
55785800 ACTTTGGATT
*
55785810 TTTTATAAA-TATTTTG-AA
1 TTTTAAAAATTATTTTGAAA
55785828 TTTTAAAAATTATTTTGAAA
1 TTTTAAAAATTATTTTGAAA
*
55785848 TTTTGAAAAT
1 TTTTAAAAAT
55785858 AAAATTGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 8 0.31
19 7 0.27
20 11 0.42
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTAAAAATTATTTTGAAA
Found at i:55788470 original size:125 final size:127
Alignment explanation
Indices: 55788222--55788481 Score: 328
Period size: 125 Copynumber: 2.1 Consensus size: 127
55788212 ATACCCCCAC
* * *
55788222 TCCTGTTTGAAGCATTTTTTTAAACTATTTACTCAAAAACGTCAACTCGAAATTATTTCTTTCAG
1 TCCTGCTTGAAGCAGTTTTTTAAACTATTTACTCAAAAACGTCAACTCGAAATTATTTCTTCCAG
* * * *
55788287 GACCAACTGTAGCAAAAGCACGTCCACGAGAGCGCAATTTCACAAATTCTTCTCATAAAGCA
66 GACCAACTGTAGCAAAAGCACATACACGAGAGCGCAACTTCACAAAATCTTCTCATAAAGCA
* * * *
55788349 TCCTGCTTGAAGC-GTTTTTTAAACTATTTGCTCAGAAATGTCAAGTCGAAATTATTT-TTCCAG
1 TCCTGCTTGAAGCAGTTTTTTAAACTATTTACTCAAAAACGTCAACTCGAAATTATTTCTTCCAG
** * * * * *
55788412 GACTTACTGTAGCAAAAGCACATACACGTGGGCGCGACTTCA-AAAATCATTCTGATAAATCA
66 GACCAACTGTAGCAAAAGCACATACACGAGAGCGCAACTTCACAAAATC-TTCTCATAAAGCA
55788474 TCCTGCTT
1 TCCTGCTT
55788482 TGATTTTATC
Statistics
Matches: 114, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
124 5 0.04
125 58 0.51
126 39 0.34
127 12 0.11
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.32
Consensus pattern (127 bp):
TCCTGCTTGAAGCAGTTTTTTAAACTATTTACTCAAAAACGTCAACTCGAAATTATTTCTTCCAG
GACCAACTGTAGCAAAAGCACATACACGAGAGCGCAACTTCACAAAATCTTCTCATAAAGCA
Found at i:55789425 original size:13 final size:14
Alignment explanation
Indices: 55789407--55789439 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
55789397 TTTGTTTAAC
55789407 TGAAAA-TAATTTT
1 TGAAAATTAATTTT
*
55789420 TGAAAATTTATTTT
1 TGAAAATTAATTTT
55789434 TGAAAA
1 TGAAAA
55789440 GTGGATTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (14 bp):
TGAAAATTAATTTT
Found at i:55791065 original size:13 final size:13
Alignment explanation
Indices: 55791047--55791072 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55791037 TATGACTATC
55791047 AAGTGTGTAGTTT
1 AAGTGTGTAGTTT
55791060 AAGTGTGTAGTTT
1 AAGTGTGTAGTTT
55791073 TATTTAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (13 bp):
AAGTGTGTAGTTT
Found at i:55791452 original size:30 final size:31
Alignment explanation
Indices: 55791416--55791476 Score: 115
Period size: 30 Copynumber: 2.0 Consensus size: 31
55791406 TCTAAAAAAG
55791416 TAAGTCATTTTATAT-AAAAAAGATTATTTT
1 TAAGTCATTTTATATAAAAAAAGATTATTTT
55791446 TAAGTCATTTTATATAAAAAAAGATTATTTT
1 TAAGTCATTTTATATAAAAAAAGATTATTTT
55791477 CCGTTTATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (31 bp):
TAAGTCATTTTATATAAAAAAAGATTATTTT
Found at i:55792813 original size:11 final size:10
Alignment explanation
Indices: 55792787--55792812 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
55792777 ACTGACTAGC
55792787 AAAAAAGAAA
1 AAAAAAGAAA
55792797 AAAAAAGAAA
1 AAAAAAGAAA
55792807 AAAAAA
1 AAAAAA
55792813 AAAGCGAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:55792951 original size:12 final size:13
Alignment explanation
Indices: 55792936--55792964 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
55792926 ATATATATAT
55792936 TCTTTCTCAT-TC
1 TCTTTCTCATCTC
55792948 TCTTTCTCATCTC
1 TCTTTCTCATCTC
55792961 TCTT
1 TCTT
55792965 CAAATTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.07, C:0.34, G:0.00, T:0.59
Consensus pattern (13 bp):
TCTTTCTCATCTC
Found at i:55796043 original size:36 final size:36
Alignment explanation
Indices: 55795954--55796043 Score: 87
Period size: 36 Copynumber: 2.5 Consensus size: 36
55795944 AAATATTTGC
* * *
55795954 ATTTATATTAAAAACATTTATTATTAAATATTTATA
1 ATTTATAATCAAAATATTTATTATTAAATATTTATA
* *
55795990 ATTTATAATCTATATATTTATTATTAAAATATTT-TA
1 ATTTATAATCAAAATATTTATTATT-AAATATTTATA
55796026 ATATT-TCAA-CAAAATATT
1 AT-TTAT-AATCAAAATATT
55796044 AAGAACGGTT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
36 32 0.73
37 12 0.27
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (36 bp):
ATTTATAATCAAAATATTTATTATTAAATATTTATA
Found at i:55798212 original size:23 final size:21
Alignment explanation
Indices: 55798186--55798252 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 21
55798176 TGTCTTTCAC
55798186 AAATTTTAGGGATTTGTTTGGCT
1 AAATTTTAGGGATTTGTTT--CT
* *
55798209 AAATTGTAGGTATTTGTCTTCT
1 AAATTTTAGGGATTTGT-TTCT
*
55798231 ACAAATTTAGGGATTTGTTTCT
1 A-AATTTTAGGGATTTGTTTCT
55798253 CTTTTATTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
22 7 0.19
23 28 0.76
24 2 0.05
ACGTcount: A:0.24, C:0.07, G:0.21, T:0.48
Consensus pattern (21 bp):
AAATTTTAGGGATTTGTTTCT
Found at i:55801380 original size:39 final size:38
Alignment explanation
Indices: 55801334--55801442 Score: 153
Period size: 39 Copynumber: 3.1 Consensus size: 38
55801324 AATAAATATA
55801334 TTTATTTTTTAATTTTAAAATATTTTTAAAATAC----
1 TTTATTTTTTAATTTTAAAATATTTTTAAAATACTTTT
55801368 --T-TTTTTTAATTTT-AAATATTTTTAAAATACTTTT
1 TTTATTTTTTAATTTTAAAATATTTTTAAAATACTTTT
55801402 TTTAATTTTTTAATTTTAAAATATTTTTAAAATACTTTT
1 TTT-ATTTTTTAATTTTAAAATATTTTTAAAATACTTTT
55801441 TT
1 TT
55801443 AAANNNNNNN
Statistics
Matches: 66, Mismatches: 0, Indels: 13
0.84 0.00 0.16
Matches are distributed among these distances:
30 17 0.26
31 12 0.18
32 1 0.02
36 1 0.02
38 12 0.18
39 23 0.35
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (38 bp):
TTTATTTTTTAATTTTAAAATATTTTTAAAATACTTTT
Found at i:55801385 original size:30 final size:31
Alignment explanation
Indices: 55801338--55801410 Score: 139
Period size: 30 Copynumber: 2.4 Consensus size: 31
55801328 AATATATTTA
55801338 TTTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTTTTAATTTTAAAATATTTTTAAAATACT
55801369 TTTTTTAATTTT-AAATATTTTTAAAATACT
1 TTTTTTAATTTTAAAATATTTTTAAAATACT
55801399 TTTTTTAATTTT
1 TTTTTTAATTTT
55801411 TTAATTTTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 30 0.71
31 12 0.29
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (31 bp):
TTTTTTAATTTTAAAATATTTTTAAAATACT
Found at i:55801418 original size:28 final size:29
Alignment explanation
Indices: 55801338--55801429 Score: 116
Period size: 30 Copynumber: 3.1 Consensus size: 29
55801328 AATATATTTA
*
55801338 TTTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTTTTAATTTT--AATAATTTTAAAATACT
*
55801369 TTTTTTAATTTTAAATATTTTTAAAATACT
1 TTTTTTAATTTT-AATAATTTTAAAATACT
*
55801399 TTTTTTAATTTT-TTAATTTTAAAATA-T
1 TTTTTTAATTTTAATAATTTTAAAATACT
55801426 TTTT
1 TTTT
55801430 AAAATACTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
27 5 0.08
28 12 0.20
30 30 0.51
31 12 0.20
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (29 bp):
TTTTTTAATTTTAATAATTTTAAAATACT
Found at i:55801440 original size:28 final size:28
Alignment explanation
Indices: 55801387--55801440 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
55801377 TTTTAAATAT
** *
55801387 TTTTAAAATACTTTTTTTAATTTTTTAA
1 TTTTAAAATACTTTTTAAAATCTTTTAA
55801415 TTTTAAAATA-TTTTTAAAATACTTTT
1 TTTTAAAATACTTTTTAAAAT-CTTTT
55801441 TTAAANNNNN
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 8 0.36
28 14 0.64
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTTAAAATACTTTTTAAAATCTTTTAA
Found at i:55802966 original size:13 final size:13
Alignment explanation
Indices: 55802950--55802976 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55802940 TATTATACAT
55802950 TTCTATCCTGAAA
1 TTCTATCCTGAAA
55802963 TTCTATCCTGAAA
1 TTCTATCCTGAAA
55802976 T
1 T
55802977 CTGAGGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (13 bp):
TTCTATCCTGAAA
Found at i:55809201 original size:58 final size:60
Alignment explanation
Indices: 55809075--55809209 Score: 143
Period size: 58 Copynumber: 2.3 Consensus size: 60
55809065 TGATTATCTT
* * * * * *
55809075 AATATTCAATTTAATTTTATATTTATCTTGTAGATAAATATTCTATTAATTTAATAGATTT
1 AATATTAAATTTAATCTAATATTTATCTTGTAGATAAACATTATATTAATTTAATA-ATTA
*
55809136 AATATTAAATTTAATCTAATATTTATC-T-T-GATAAGCATTATATTAATTTAAT-ATTA
1 AATATTAAATTTAATCTAATATTTATCTTGTAGATAAACATTATATTAATTTAATAATTA
*
55809192 AAGTGATTAAGTTTAATC
1 AA-T-ATTAAATTTAATC
55809210 ATAGTTGAAC
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
56 5 0.08
57 1 0.02
58 32 0.50
59 1 0.02
60 1 0.02
61 24 0.38
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.49
Consensus pattern (60 bp):
AATATTAAATTTAATCTAATATTTATCTTGTAGATAAACATTATATTAATTTAATAATTA
Found at i:55810961 original size:84 final size:84
Alignment explanation
Indices: 55810799--55811080 Score: 266
Period size: 84 Copynumber: 3.3 Consensus size: 84
55810789 GCACATCAAT
** * ** * *
55810799 CTAGCACCGTAGTGCATCATCAAATAAACCGAAGGA-AAT-GGACTGTCACCTATAGTGCATCAT
1 CTAGCACCAAAGTGCATCATCGAATAAACCGAA--ACAATCATACTGGCACATA-AGTGCATCAT
* * *
55810862 TGGACAATCCAAAGCAATTATA
63 TGGATAAACCAAAGCAAATATA
* * * ** *
55810884 CTAGCACGCAAAATGCATCATCGGATGAACCG-AATGATCATACTGGTACATAAGTGCATCATTG
1 CTAGCAC-CAAAGTGCATCATCGAATAAACCGAAACAATCATACTGGCACATAAGTGCATCATTG
** **
55810948 GATAAACTGAAGCAACCATA
65 GATAAACCAAAGCAAATATA
*
55810968 CTAGCA-CATAAGTGCATCATCGAATAAACCGAAACAATCATACTGGCACATAAATGCATCATTG
1 CTAGCACCA-AAGTGCATCATCGAATAAACCGAAACAATCATACTGGCACATAAGTGCATCATTG
55811032 GATAAACCAAAGCAAATATA
65 GATAAACCAAAGCAAATATA
* * *
55811052 CTGGCACACATAGTGCATCATCGACTAAA
1 CTAGCAC-CAAAGTGCATCATCGAATAAA
55811081 TCAAAGTATA
Statistics
Matches: 158, Mismatches: 32, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
82 2 0.01
83 20 0.13
84 83 0.53
85 33 0.21
86 20 0.13
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.21
Consensus pattern (84 bp):
CTAGCACCAAAGTGCATCATCGAATAAACCGAAACAATCATACTGGCACATAAGTGCATCATTGG
ATAAACCAAAGCAAATATA
Found at i:55810968 original size:42 final size:42
Alignment explanation
Indices: 55810852--55811072 Score: 187
Period size: 42 Copynumber: 5.2 Consensus size: 42
55810842 TGTCACCTAT
* * * ** *
55810852 AGTGCATCATTGGACAATCCAAAGCAATTATACTAGCACGCA-A
1 AGTGCATCATTGGATAAACCGAAGCAAACATACTGGCA--CATA
* * * * *
55810895 AATGCATCATCGGATGAACCGAATG--ATCATACTGGTACATA
1 AGTGCATCATTGGATAAACCGAA-GCAAACATACTGGCACATA
* * *
55810936 AGTGCATCATTGGATAAACTGAAGCAACCATACTAGCACATA
1 AGTGCATCATTGGATAAACCGAAGCAAACATACTGGCACATA
* * * *
55810978 AGTGCATCATCGAATAAACCGAAACAATCATACTGGCACATA
1 AGTGCATCATTGGATAAACCGAAGCAAACATACTGGCACATA
* * * *
55811020 AATGCATCATTGGATAAACCAAAGCAAATATACTGGCACACA
1 AGTGCATCATTGGATAAACCGAAGCAAACATACTGGCACATA
55811062 TAGTGCATCAT
1 -AGTGCATCAT
55811073 CGACTAAATC
Statistics
Matches: 142, Mismatches: 31, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
40 3 0.02
41 20 0.14
42 92 0.65
43 26 0.18
44 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (42 bp):
AGTGCATCATTGGATAAACCGAAGCAAACATACTGGCACATA
Found at i:55812017 original size:13 final size:13
Alignment explanation
Indices: 55811995--55812034 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
55811985 TAATTTTCGA
55811995 TTTCAAGTCCAAT
1 TTTCAAGTCCAAT
*
55812008 TTTTAAGTCCAAT
1 TTTCAAGTCCAAT
*
55812021 TTTCAAGTTCAAT
1 TTTCAAGTCCAAT
55812034 T
1 T
55812035 ACCCATTGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.30, C:0.17, G:0.07, T:0.45
Consensus pattern (13 bp):
TTTCAAGTCCAAT
Found at i:55812796 original size:25 final size:24
Alignment explanation
Indices: 55812768--55812814 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
55812758 TATAGTTCAA
55812768 ATCA-CAATCCTATCATTCTCAATTC
1 ATCATCAATCC-ATCATT-TCAATTC
*
55812793 ATCATCAATTCATCATTTCAAT
1 ATCATCAATCCATCATTTCAAT
55812815 ACAATATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 5 0.25
25 10 0.50
26 5 0.25
ACGTcount: A:0.34, C:0.28, G:0.00, T:0.38
Consensus pattern (24 bp):
ATCATCAATCCATCATTTCAATTC
Found at i:55815617 original size:24 final size:24
Alignment explanation
Indices: 55815573--55815618 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
55815563 ATGGTTTTTT
*
55815573 AAATAATTATTAATTTTTTAAAAA
1 AAATAATTATTAATTTCTTAAAAA
*
55815597 AAATATATTTTTAA-TTCTTAAA
1 AAATA-ATTATTAATTTCTTAAA
55815619 TAGGCACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAATAATTATTAATTTCTTAAAAA
Found at i:55815900 original size:28 final size:30
Alignment explanation
Indices: 55815817--55815903 Score: 74
Period size: 29 Copynumber: 3.0 Consensus size: 30
55815807 ACCAATTAAT
* * *
55815817 TAATTTTTTTA-AA-ATAAAAATATTGAAAA
1 TAATTTTTTTAGAATTTATAAA-ATTAAAAA
* **
55815846 TAATTTTTTTATAATTTATAATTTTAAAAA
1 TAATTTTTTTAGAATTTATAAAATTAAAAA
*
55815876 T-ATTTTTTT-GAATTTTTAAAATTAAAAA
1 TAATTTTTTTAGAATTTATAAAATTAAAAA
55815904 ATTAAAAAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
28 15 0.32
29 19 0.40
30 9 0.19
31 4 0.09
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (30 bp):
TAATTTTTTTAGAATTTATAAAATTAAAAA
Found at i:55825138 original size:31 final size:31
Alignment explanation
Indices: 55825103--55825161 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
55825093 AACAATCCGA
*
55825103 TGACTTAAATAAAATTTTTTGAATAGTTTCG
1 TGACTTAAATAAAATTTTTCGAATAGTTTCG
55825134 TGACTTAAATAAAATTTTTCGAATAGTT
1 TGACTTAAATAAAATTTTTCGAATAGTT
55825162 AAATGATCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (31 bp):
TGACTTAAATAAAATTTTTCGAATAGTTTCG
Found at i:55829165 original size:20 final size:20
Alignment explanation
Indices: 55829121--55829188 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
55829111 GCCCTATGGG
55829121 AAAAGCACAGCAAAG-GAAAA
1 AAAAGCACAGCAAAGTG-AAA
*
55829141 AAAAGTACAGCAAAGTGAAA
1 AAAAGCACAGCAAAGTGAAA
* * * *
55829161 AAAAGGAGAGCAAAATTAAA
1 AAAAGCACAGCAAAGTGAAA
55829181 AAAAGCAC
1 AAAAGCAC
55829189 TGCCAATAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 39 0.98
21 1 0.03
ACGTcount: A:0.63, C:0.12, G:0.19, T:0.06
Consensus pattern (20 bp):
AAAAGCACAGCAAAGTGAAA
Done.