Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009247.1 Hibiscus syriacus cultivar Beakdansim tig00112888_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: 1479039
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 8
Found at i:1304149 original size:15 final size:16
Alignment explanation
Indices: 1304129--1304158 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1304119 TGTTTTCGAC
1304129 TTCTTTTATT-TTTTA
1 TTCTTTTATTCTTTTA
1304144 TTCTTTTATTCTTTT
1 TTCTTTTATTCTTTT
1304159 TTTTGTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (16 bp):
TTCTTTTATTCTTTTA
Found at i:1304152 original size:8 final size:8
Alignment explanation
Indices: 1304129--1304158 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
1304119 TGTTTTCGAC
1304129 TTCTTTTA
1 TTCTTTTA
1304137 TT-TTTTA
1 TTCTTTTA
1304144 TTCTTTTA
1 TTCTTTTA
1304152 TTCTTTT
1 TTCTTTT
1304159 TTTTGTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (8 bp):
TTCTTTTA
Found at i:1307115 original size:19 final size:19
Alignment explanation
Indices: 1307087--1307125 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1307077 AAAATATGCC
*
1307087 TGCTGTTGCTATTATTGTT
1 TGCTGCTGCTATTATTGTT
*
1307106 TGCTGCTGCTATTGTTGTT
1 TGCTGCTGCTATTATTGTT
1307125 T
1 T
1307126 CTACTGCTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.08, C:0.13, G:0.23, T:0.56
Consensus pattern (19 bp):
TGCTGCTGCTATTATTGTT
Found at i:1307157 original size:17 final size:16
Alignment explanation
Indices: 1307123--1307157 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1307113 GCTATTGTTG
*
1307123 TTTCTACTGCTTCTGC
1 TTTCTACTGCTGCTGC
1307139 TTTCTACTGCCTGCTGC
1 TTTCTACTG-CTGCTGC
1307156 TT
1 TT
1307158 GTTGCCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.06, C:0.31, G:0.14, T:0.49
Consensus pattern (16 bp):
TTTCTACTGCTGCTGC
Found at i:1307441 original size:11 final size:11
Alignment explanation
Indices: 1307420--1307459 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
1307410 TTGTATTGAC
1307420 TTAAATGTTAT
1 TTAAATGTTAT
* *
1307431 TCAAATTTTAT
1 TTAAATGTTAT
1307442 ATTAAATGTTAT
1 -TTAAATGTTAT
1307454 TTAAAT
1 TTAAAT
1307460 TATAATTATC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.53
Consensus pattern (11 bp):
TTAAATGTTAT
Found at i:1307735 original size:23 final size:24
Alignment explanation
Indices: 1307708--1307757 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
1307698 TTATGTTTTC
*
1307708 TTTATATAAATTAAATTATA-TAA
1 TTTATATAAATTAAACTATATTAA
1307731 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
1307755 TTT
1 TTT
1307758 TTCTTTGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:1307950 original size:20 final size:19
Alignment explanation
Indices: 1307925--1307963 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1307915 ACATCATAAG
1307925 TTAAAAAACTCATAATTTTA
1 TTAAAAAA-TCATAATTTTA
* *
1307945 TTAAAATATTATAATTTTA
1 TTAAAAAATCATAATTTTA
1307964 CCCATGATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAAAAAATCATAATTTTA
Found at i:1308053 original size:16 final size:16
Alignment explanation
Indices: 1308034--1308083 Score: 100
Period size: 16 Copynumber: 3.1 Consensus size: 16
1308024 TACAGCTCAA
1308034 GTTAAAAACAGGTCGG
1 GTTAAAAACAGGTCGG
1308050 GTTAAAAACAGGTCGG
1 GTTAAAAACAGGTCGG
1308066 GTTAAAAACAGGTCGG
1 GTTAAAAACAGGTCGG
1308082 GT
1 GT
1308084 AATACCAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.36, C:0.12, G:0.32, T:0.20
Consensus pattern (16 bp):
GTTAAAAACAGGTCGG
Found at i:1309600 original size:2 final size:2
Alignment explanation
Indices: 1309593--1309620 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1309583 TGAAAGTTCA
1309593 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
1309621 CAACCTCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1310059 original size:3 final size:3
Alignment explanation
Indices: 1310051--1310080 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1310041 TGAATTTTGA
1310051 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1310081 ATTTCTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1310818 original size:2 final size:2
Alignment explanation
Indices: 1310811--1310893 Score: 96
Period size: 2 Copynumber: 41.0 Consensus size: 2
1310801 CTTATTTATT
1310811 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
* * * * *
1310853 TA CTA -A TG TA CA TA CA TCA TA CA TA TA TA TT TA TA TA TA TA
1 TA -TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
1310894 CACACACATA
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
1 1 0.01
2 63 0.93
3 4 0.06
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1311016 original size:2 final size:2
Alignment explanation
Indices: 1311009--1311053 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1310999 TTTATTTCAA
1311009 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
1311051 AT A
1 AT A
1311054 AGTATAACGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1313770 original size:5 final size:5
Alignment explanation
Indices: 1313764--1313829 Score: 114
Period size: 5 Copynumber: 13.2 Consensus size: 5
1313754 TATAGGGCAG
* *
1313764 GGTAG GGTAG GGTAT GGTAT GGTAT GGTAT GGTAT GGTAT GGTAT GGTAT
1 GGTAT GGTAT GGTAT GGTAT GGTAT GGTAT GGTAT GGTAT GGTAT GGTAT
1313814 GGTAT GGTAT GGTAT G
1 GGTAT GGTAT GGTAT G
1313830 ATATAATATG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 60 1.00
ACGTcount: A:0.20, C:0.00, G:0.44, T:0.36
Consensus pattern (5 bp):
GGTAT
Found at i:1313881 original size:22 final size:22
Alignment explanation
Indices: 1313853--1313930 Score: 79
Period size: 23 Copynumber: 3.5 Consensus size: 22
1313843 TTTCCAATAT
1313853 ATATATAATATAGTTTTGAAAA
1 ATATATAATATAGTTTTGAAAA
* *
1313875 ATATATAAAATTATTTTTGAAATA
1 ATATATAATA-TAGTTTTGAAA-A
* *
1313899 ATAT-T-ATATAGTTTTTAAAT
1 ATATATAATATAGTTTTGAAAA
1313919 ATATATATATAT
1 ATATATA-ATAT
1313931 TATATTATTA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 4 0.09
21 10 0.22
22 11 0.24
23 15 0.33
24 5 0.11
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (22 bp):
ATATATAATATAGTTTTGAAAA
Found at i:1313901 original size:24 final size:24
Alignment explanation
Indices: 1313851--1313925 Score: 70
Period size: 24 Copynumber: 3.3 Consensus size: 24
1313841 AGTTTCCAAT
*
1313851 ATATATATAATATAGTTTTGAAAA
1 ATATATAAAATATAGTTTTGAAAA
*
1313875 ATATATAAAAT-TATTTTTGAAATA
1 ATATATAAAATATAGTTTTGAAA-A
* *
1313899 ATAT-T---ATATAGTTTTTAAAT
1 ATATATAAAATATAGTTTTGAAAA
1313919 ATATATA
1 ATATATA
1313926 TATATTATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
20 6 0.14
21 10 0.24
23 11 0.26
24 15 0.36
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (24 bp):
ATATATAAAATATAGTTTTGAAAA
Found at i:1313965 original size:23 final size:21
Alignment explanation
Indices: 1313935--1313979 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
1313925 ATATATTATA
*
1313935 TTATTATTACTATTTTCTTTTT
1 TTATTATT-CTATTTTATTTTT
*
1313957 TTATCTATTTTATTTTATTTTT
1 TTAT-TATTCTATTTTATTTTT
1313979 T
1 T
1313980 AATTTCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.76
Consensus pattern (21 bp):
TTATTATTCTATTTTATTTTT
Found at i:1333820 original size:158 final size:155
Alignment explanation
Indices: 1333395--1333943 Score: 627
Period size: 156 Copynumber: 3.5 Consensus size: 155
1333385 AGTTACATAG
* * * * * * *
1333395 GTATTCTATTGTGGTATATGAGCATGTGGTTTAAATTTGGTAAAAAAAAAGACTTAAAATAAATG
1 GTATTCTACTATGGTTTAGGAGCATGTGATTCAAATTTGGT-AAAAAAATGACTTAAAATAAATG
** * * *
1333460 ACAAATTGAAGGAATAAGGAGATTATGAAAGATTGAAGGACTAAATTGAAAAATAAAAAATAT-A
65 ATGAATTGAAGAAATAAGGAGATTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAA-ATGT
* *
1333524 TATCAAAAAGAGGAATTGAAATTACACAT
129 TATTAAAAAGAGG-ATTGAAA-TAAACAT
** * * **
1333553 GTATTCTACTATGGTTTAGGAGCATGTGGCTC-AATTTTGTTAAAAACGGACTTAAAATAAATGA
1 GTATTCTACTATGGTTTAGGAGCATGTGATTCAAATTTGGTAAAAAAATGACTTAAAATAAATGA
* **
1333617 TGAATTGAAGAAATAAGGAGATTATGAAAATTTGAATAACTAAATTGAAAAATAAAAAAATGTTA
66 TGAATTGAAGAAATAAGGAGATTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAAATGTTA
* * **
1333682 TTTAAAAGAGGCATTAAAAGTGTACAT
131 TTAAAAAGAGG-ATTGAAA-TAAACAT
* *
1333709 GTATTATGCTATGGTTTAGGAGCATGTGATTCAAATTTGGTAAAAAAAATGACTTAAAATAAATG
1 GTATTCTACTATGGTTTAGGAGCATGTGATTCAAATTTGGT-AAAAAAATGACTTAAAATAAATG
* * ** *
1333774 ATGAATTGAGGAAATAATGTTATTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAATTGTT
65 ATGAATTGAAGAAATAAGGAGATTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAAATGTT
* *
1333839 ATCATAAAGA-GATTGAAATAAACAT
130 ATTAAAAAGAGGATTGAAATAAACAT
* * * * *
1333864 GCATTCTACTATAGTTTAGGAGCATGTGATTCAAATTTGATAAAAAAATAGACTTAGAATGAATG
1 GTATTCTACTATGGTTTAGGAGCATGTGATTCAAATTTGGTAAAAAAAT-GACTTAAAATAAATG
*
1333929 AGGAATTGAAGAAAT
65 ATGAATTGAAGAAAT
1333944 TATGAAATCA
Statistics
Matches: 331, Mismatches: 56, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
154 8 0.02
155 69 0.21
156 129 0.39
157 15 0.05
158 110 0.33
ACGTcount: A:0.46, C:0.06, G:0.18, T:0.30
Consensus pattern (155 bp):
GTATTCTACTATGGTTTAGGAGCATGTGATTCAAATTTGGTAAAAAAATGACTTAAAATAAATGA
TGAATTGAAGAAATAAGGAGATTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAAATGTTA
TTAAAAAGAGGATTGAAATAAACAT
Found at i:1335804 original size:7 final size:8
Alignment explanation
Indices: 1335779--1335803 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1335769 CCCTGTCATC
1335779 AAGATAAA
1 AAGATAAA
1335787 AAGATAAA
1 AAGATAAA
1335795 AAGATAAA
1 AAGATAAA
1335803 A
1 A
1335804 GGCAATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (8 bp):
AAGATAAA
Found at i:1338290 original size:13 final size:13
Alignment explanation
Indices: 1338272--1338296 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1338262 TAAACTTACA
1338272 TTTTTTTTTTTTC
1 TTTTTTTTTTTTC
1338285 TTTTTTTTTTTT
1 TTTTTTTTTTTT
1338297 TGTTATAACA
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:0.00, C:0.04, G:0.00, T:0.96
Consensus pattern (13 bp):
TTTTTTTTTTTTC
Found at i:1349124 original size:23 final size:23
Alignment explanation
Indices: 1349095--1349158 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
1349085 CAACTCGTAT
*
1349095 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACATAG
* * * *
1349118 AATTGCACTGTAGTGCCGCATAG
1 AAATGCACCGAAGTGCCACATAG
1349141 AAATGCACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
1349159 TATAAGATAT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.17
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACATAG
Found at i:1354067 original size:48 final size:48
Alignment explanation
Indices: 1353990--1354100 Score: 120
Period size: 48 Copynumber: 2.3 Consensus size: 48
1353980 TATTCTATCG
* * * ** *
1353990 TTATTTATATATATATATATACTTTTAATTCT-TTTTCATATATCATTA
1 TTATTTATATATATTTATATACTTATAATTATACATT-ATATATAATTA
*
1354038 TTATTTATATATATTTTTATTAC-TATAATTATACATTATATATAATTA
1 TTATTTATATATATTTATA-TACTTATAATTATACATTATATATAATTA
1354086 TTATTT-TATATATTT
1 TTATTTATATATATTT
1354101 CATTTTATCT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
47 9 0.17
48 40 0.74
49 5 0.09
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (48 bp):
TTATTTATATATATTTATATACTTATAATTATACATTATATATAATTA
Found at i:1354097 original size:16 final size:16
Alignment explanation
Indices: 1354028--1354097 Score: 56
Period size: 16 Copynumber: 4.4 Consensus size: 16
1354018 TTCTTTTTCA
*
1354028 TATATCATTATTA-TT
1 TATATAATTATTATTT
*
1354043 TATATATATT-TT-TAT
1 TATATA-ATTATTATTT
* *
1354058 TACTATAATTATACATTA
1 TA-TATAATTAT-TATTT
1354076 TATATAATTATTATTT
1 TATATAATTATTATTT
1354092 TATATA
1 TATATA
1354098 TTTCATTTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 11
0.70 0.12 0.18
Matches are distributed among these distances:
15 13 0.31
16 17 0.40
17 9 0.21
18 3 0.07
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATAATTATTATTT
Found at i:1354123 original size:15 final size:15
Alignment explanation
Indices: 1354103--1354134 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1354093 ATATATTTCA
*
1354103 TTTTATCTTTTATTT
1 TTTTATCTTCTATTT
1354118 TTTTATCTTCTATTT
1 TTTTATCTTCTATTT
1354133 TT
1 TT
1354135 ATTTTTGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTATCTTCTATTT
Found at i:1354151 original size:20 final size:20
Alignment explanation
Indices: 1354104--1354157 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
1354094 TATATTTCAT
*
1354104 TTTATCTTTTATTTTTTTATC
1 TTTAT-TTTTATTTTTGTATC
1354125 TTCTATTTTTATTTTTGTAT-
1 TT-TATTTTTATTTTTGTATC
*
1354145 TGTTATTATTATT
1 T-TTATTTTTATT
1354158 ATCTTCTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 10 0.34
21 16 0.55
22 3 0.10
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.74
Consensus pattern (20 bp):
TTTATTTTTATTTTTGTATC
Found at i:1354185 original size:2 final size:2
Alignment explanation
Indices: 1354178--1354211 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1354168 TTTTATGTAT
1354178 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1354212 TTGTTTTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1357310 original size:27 final size:27
Alignment explanation
Indices: 1357280--1357335 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
1357270 GCCTGTCATC
*
1357280 TTCATGGCCTAGCAAGGGAAGGTGGAG
1 TTCATGGCCTAGCAAGGGAAGCTGGAG
1357307 TTCATGGCCTAGCAAGGGAAGCTGGAG
1 TTCATGGCCTAGCAAGGGAAGCTGGAG
1357334 TT
1 TT
1357336 GTTTGACAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.16, G:0.38, T:0.21
Consensus pattern (27 bp):
TTCATGGCCTAGCAAGGGAAGCTGGAG
Found at i:1364666 original size:110 final size:106
Alignment explanation
Indices: 1364575--1364777 Score: 246
Period size: 110 Copynumber: 1.9 Consensus size: 106
1364565 AGAGGCTTCC
* * * ** * *
1364575 CAATTTCAACTTCACAACGAGGGATATTGGACTCAAGATAACACAAGCTCAACTTCACAACGAAG
1 CAATTTCAACTTCACAACAAAGAATATTAAACTCAAGACAACACAAGCTCAACATCACAACGAAG
* ***
1364640 GGGCGACTGATTGTCAACAAACAACTTTTCAGTTTCATTCAGAGT
66 GGGCGACTGACTGTCAACAAACAAC-TTTCAG--T-AAGAAGAGT
*
1364685 CAATTTCAACTTCACAGCAAAGAATATTAAACTCAAGACAACACAAGCTCAACATCACAACGAAG
1 CAATTTCAACTTCACAACAAAGAATATTAAACTCAAGACAACACAAGCTCAACATCACAACGAAG
*
1364750 GGGCGGCTGACTGTCAACAAACAA-TTTC
66 GGGCGACTGACTGTCAACAAACAACTTTC
1364778 CAGAGCCAAT
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
108 4 0.05
110 79 0.95
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (106 bp):
CAATTTCAACTTCACAACAAAGAATATTAAACTCAAGACAACACAAGCTCAACATCACAACGAAG
GGGCGACTGACTGTCAACAAACAACTTTCAGTAAGAAGAGT
Found at i:1366191 original size:2 final size:2
Alignment explanation
Indices: 1366186--1366228 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1366176 TTATTATTCT
1366186 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
1366228 T
1 T
1366229 TATCTTCATT
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:1366290 original size:2 final size:2
Alignment explanation
Indices: 1366283--1366308 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1366273 TATCGTTATT
1366283 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
1366309 CTTTTAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1366390 original size:17 final size:17
Alignment explanation
Indices: 1366320--1366392 Score: 54
Period size: 17 Copynumber: 4.6 Consensus size: 17
1366310 TTTTAATTCT
1366320 TTTTCATATATCATTATTA
1 TTTT-ATATAT-ATTATTA
1366339 -TTTATATAT-TT-TTA
1 TTTTATATATATTATTA
1366353 --TTACTATA-A-TA-TA
1 TTTTA-TATATATTATTA
*
1366366 TGTTATATATATTATTA
1 TTTTATATATATTATTA
1366383 TTTTATATAT
1 TTTTATATAT
1366393 TTCATTTTAT
Statistics
Matches: 45, Mismatches: 1, Indels: 18
0.70 0.02 0.28
Matches are distributed among these distances:
13 6 0.13
14 11 0.24
15 6 0.13
16 2 0.04
17 17 0.38
18 3 0.07
ACGTcount: A:0.34, C:0.04, G:0.01, T:0.60
Consensus pattern (17 bp):
TTTTATATATATTATTA
Found at i:1366418 original size:15 final size:15
Alignment explanation
Indices: 1366397--1366428 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1366387 ATATATTTCA
*
1366397 TTTTATCTTTTATTT
1 TTTTATCTTCTATTT
1366412 TTTTATCTTCTATTT
1 TTTTATCTTCTATTT
1366427 TT
1 TT
1366429 ATTTTTGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTATCTTCTATTT
Found at i:1366445 original size:20 final size:20
Alignment explanation
Indices: 1366398--1366451 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
1366388 TATATTTCAT
*
1366398 TTTATCTTTTATTTTTTTATC
1 TTTAT-TTTTATTTTTGTATC
1366419 TTCTATTTTTATTTTTGTAT-
1 TT-TATTTTTATTTTTGTATC
*
1366439 TGTTATTGTTATT
1 T-TTATTTTTATT
1366452 ATCTTCTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 10 0.34
21 16 0.55
22 3 0.10
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.74
Consensus pattern (20 bp):
TTTATTTTTATTTTTGTATC
Found at i:1371219 original size:20 final size:20
Alignment explanation
Indices: 1371171--1371221 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1371161 ATAACTGTAA
*
1371171 GGTGCATCAATGCATTCAGG
1 GGTGCATCGATGCATTCAGG
1371191 GGTGCATCGATGCATTCAGG
1 GGTGCATCGATGCATTCAGG
*
1371211 GGTTCATCGAT
1 GGTGCATCGAT
1371222 ACACACAGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.27
Consensus pattern (20 bp):
GGTGCATCGATGCATTCAGG
Found at i:1371230 original size:20 final size:20
Alignment explanation
Indices: 1371187--1371230 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1371177 TCAATGCATT
* **
1371187 CAGGGGTGCATCGATGCATT
1 CAGGGGTGCATCGATACACA
*
1371207 CAGGGGTTCATCGATACACA
1 CAGGGGTGCATCGATACACA
1371227 CAGG
1 CAGG
1371231 CAGGCATCGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.23, G:0.32, T:0.20
Consensus pattern (20 bp):
CAGGGGTGCATCGATACACA
Found at i:1373475 original size:21 final size:21
Alignment explanation
Indices: 1373449--1373489 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1373439 GAAATTACTA
1373449 TAGCAGTGCATCGATACACAG
1 TAGCAGTGCATCGATACACAG
1373470 TAGCAGTGCATCGATACACA
1 TAGCAGTGCATCGATACACA
1373490 TTTTAAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (21 bp):
TAGCAGTGCATCGATACACAG
Found at i:1375853 original size:198 final size:196
Alignment explanation
Indices: 1375513--1376074 Score: 689
Period size: 198 Copynumber: 2.8 Consensus size: 196
1375503 ACTTTTTTAC
* ***
1375513 TGTGACTAAATAATTTTTTTACAATTTGGCATTGTGAAAGAATATTATTTGTCACAATTTTTTAT
1 TGTGACTAAATAATTTTGTTACAATTTATTATTGTGAAAGAATATTATTTGTCACAATTTTTTAT
* * *
1375578 AATGAGAAATTAGTATTTGTTATAAATTGTTATTTTGATTAAATAAATTTGTCACAATTTTTTAT
66 -ATGTGAAATTAATATTTGTTATAAATTGTTATTTTGATTAAATAAATTTGTC-CAAATTTTTAT
* *** *
1375643 TTTGCCAAAATATTGGGACGAAATAAATTTGACATAATTGTTTACTTTGACTAAAGTTAATGTGT
129 TTTGACAAAATATTGGGACGAAATAAATTTGACATAAAAATTTACTTTGACTAAAGTTAATATGT
1375708 TAT
194 TAT
* * * *
1375711 TGTGACTAAATCATTTTGTTGCAATTTATTATTGTGAAATAATATTACTTGTCACAATTTTTTAT
1 TGTGACTAAATAATTTTGTTACAATTTATTATTGTGAAAGAATATTATTTGTCACAATTTTTTAT
* * *
1375776 GATGTGAAATTAATATTTTTTATAAATTATTATTTTGATTAAATAAATTTTTCCGAAATTTTTAT
66 -ATGTGAAATTAATATTTGTTATAAATTGTTATTTTGATTAAATAAATTTGTCC-AAATTTTTAT
* * * * *
1375841 TTTGATAAAATATTGTGG-CAAAATAAATTTGACATAAAAATTTATTTTGACTAAATTTACTATG
129 TTTGACAAAATATTG-GGACGAAATAAATTTGACATAAAAATTTACTTTGACTAAAGTTAATATG
1375905 TTAT
193 TTAT
* * * * * *
1375909 TGTAACTAAATAAATTTGTTACAATTTATTATCGTGAAAGAATATTATTTGTCATAACTTTTAAT
1 TGTGACTAAATAATTTTGTTACAATTTATTATTGTGAAAGAATATTATTTGTCACAATTTTTTAT
* * *
1375974 AT-TGATAAATTAATATTTGTTATAAATTGTTATTATGACTAAATAAATTTGTCAAAAGTTATTT
66 ATGTG--AAATTAATATTTGTTATAAATTGTTATTTTGATTAAATAAATTTGTCCAAA-TT-TTT
* * * *
1376038 -TTTTGAGAAAATTTTGTGACGAAATAAATTTAACATA
127 ATTTTGACAAAATATTGGGACGAAATAAATTTGACATA
1376075 CTCTTGAAAT
Statistics
Matches: 311, Mismatches: 46, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
196 2 0.01
197 7 0.02
198 297 0.95
199 5 0.02
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (196 bp):
TGTGACTAAATAATTTTGTTACAATTTATTATTGTGAAAGAATATTATTTGTCACAATTTTTTAT
ATGTGAAATTAATATTTGTTATAAATTGTTATTTTGATTAAATAAATTTGTCCAAATTTTTATTT
TGACAAAATATTGGGACGAAATAAATTTGACATAAAAATTTACTTTGACTAAAGTTAATATGTTA
T
Found at i:1375991 original size:33 final size:33
Alignment explanation
Indices: 1375949--1376027 Score: 83
Period size: 33 Copynumber: 2.4 Consensus size: 33
1375939 ATCGTGAAAG
* *
1375949 AATATTATTTGTCATAACTT-TTAATATTGA-TA
1 AATAATATTTGTCATAAATTGTTAATA-TGACTA
* *
1375981 AATTAATATTTGTTATAAATTGTTATTATGACTA
1 AA-TAATATTTGTCATAAATTGTTAATATGACTA
1376015 AATAA-ATTTGTCA
1 AATAATATTTGTCA
1376028 AAAGTTATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
32 9 0.23
33 21 0.54
34 9 0.23
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (33 bp):
AATAATATTTGTCATAAATTGTTAATATGACTA
Found at i:1383503 original size:19 final size:19
Alignment explanation
Indices: 1383476--1383512 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1383466 ATGACCAACA
*
1383476 AAATAGCAATGCGATCTCT
1 AAATAGCAACGCGATCTCT
*
1383495 AAATCGCAACGCGATCTC
1 AAATAGCAACGCGATCTC
1383513 CAGCATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATAGCAACGCGATCTCT
Found at i:1383561 original size:20 final size:20
Alignment explanation
Indices: 1383538--1383649 Score: 136
Period size: 20 Copynumber: 5.6 Consensus size: 20
1383528 GTTTCCAGAT
* *
1383538 TCGCAGCGCGATTTTGACTA
1 TCGCAACGCGATTCTGACTA
* * * *
1383558 TCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTCTG-ACTA
1383578 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
1383598 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
* *
1383618 TCACAACGCGATTTTGACTA
1 TCGCAACGCGATTCTGACTA
1383638 TCGCAACGCGAT
1 TCGCAACGCGAT
1383650 AATACAAAAT
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
19 1 0.01
20 76 0.97
21 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:1383582 original size:40 final size:40
Alignment explanation
Indices: 1383538--1383673 Score: 143
Period size: 40 Copynumber: 3.4 Consensus size: 40
1383528 GTTTCCAGAT
* *
1383538 TCGCAGCGCGATTTTGACTATCGCAATGCGAATATGTA-AA
1 TCGCAACGCGATTTTGACTATCGCAACGCGAATATG-ACAA
* * * *
1383578 TCGCAACGCGATTCTGACTATCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTTTGACTATCGCAACGCGAATATGACAA
*
1383618 TCACAACGCGATTTTGACTATCGCAACGCG-ATAAT-ACAAAA
1 TCGCAACGCGATTTTGACTATCGCAACGCGAAT-ATGAC--AA
*
1383659 TCGCAATGCGATTTT
1 TCGCAACGCGATTTT
1383674 CAAAGCGCCA
Statistics
Matches: 79, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
39 4 0.05
40 61 0.77
41 14 0.18
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.26
Consensus pattern (40 bp):
TCGCAACGCGATTTTGACTATCGCAACGCGAATATGACAA
Found at i:1383860 original size:22 final size:22
Alignment explanation
Indices: 1383815--1383865 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1383805 CTACGGCGAC
*
1383815 ATCCGTCCCCATCTCCGACAAA
1 ATCCGTCCCCATCTCCAACAAA
*
1383837 ATCCGTCCCCATCTCCAACGAA
1 ATCCGTCCCCATCTCCAACAAA
*
1383859 ATTCGTC
1 ATCCGTC
1383866 TATCTCCATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.25, C:0.43, G:0.10, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCAACAAA
Found at i:1384279 original size:20 final size:19
Alignment explanation
Indices: 1384256--1384356 Score: 59
Period size: 20 Copynumber: 5.4 Consensus size: 19
1384246 TCAAATTCAC
1384256 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCA-TTTCGT
** *
1384276 GTTGCGATTTTCATTTCGC
1 GTTGCGATAGTCATTTCGT
*
1384295 GTTGCGAT--T-ATCTC--
1 GTTGCGATAGTCATTTCGT
* * *
1384309 GTCGCGATAGTCAAATTCGA
1 GTTGCGATAGTC-ATTTCGT
* *
1384329 GTTACGATAGTCATTTTCAT
1 GTTGCGATAGTCA-TTTCGT
1384349 GTTGCGAT
1 GTTGCGAT
1384357 TTTAAGTTTC
Statistics
Matches: 61, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
14 7 0.11
16 5 0.08
17 1 0.02
18 3 0.05
19 14 0.23
20 31 0.51
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.41
Consensus pattern (19 bp):
GTTGCGATAGTCATTTCGT
Found at i:1384298 original size:19 final size:20
Alignment explanation
Indices: 1384255--1384303 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
1384245 GTCAAATTCA
*
1384255 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
1384275 TGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTGTCATTTTCG
1384294 CGTTGCGATT
1 CGTTGCGATT
1384304 ATCTCGTCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:1384378 original size:73 final size:73
Alignment explanation
Indices: 1384240--1384378 Score: 174
Period size: 73 Copynumber: 1.9 Consensus size: 73
1384230 AAAATCACAA
* * * * ***
1384240 CGATAGTCAAATTCACGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTCGCGTTGCGATTA
1 CGATAGTCAAATTCACGTTACGATAGTCATTTTCATGTTGCGATTTTAATTTCGAGAAACGATTA
1384305 TCTCGTCG
66 TCTCGTCG
*
1384313 CGATAGTCAAATTCGA-GTTACGATAGTCATTTTCATGTTGCGATTTTAAGTTTC-AGAAACTAT
1 CGATAGTCAAATTC-ACGTTACGATAGTCATTTTCATGTTGCGATTTTAA-TTTCGAGAAACGAT
1384376 TAT
64 TAT
1384379 TCTTCTACAA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
73 51 0.91
74 5 0.09
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (73 bp):
CGATAGTCAAATTCACGTTACGATAGTCATTTTCATGTTGCGATTTTAATTTCGAGAAACGATTA
TCTCGTCG
Found at i:1385241 original size:23 final size:23
Alignment explanation
Indices: 1385215--1385270 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
1385205 AAAATTATAA
1385215 TTATGAAAAATATATTAATTTAT
1 TTATGAAAAATATATTAATTTAT
* *
1385238 TTAT-AAATAAAATATTTATTTAT
1 TTATGAAA-AATATATTAATTTAT
1385261 TTA-GAAAAAT
1 TTATGAAAAAT
1385271 CAGAAAATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 5 0.18
23 23 0.82
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (23 bp):
TTATGAAAAATATATTAATTTAT
Found at i:1385355 original size:20 final size:19
Alignment explanation
Indices: 1385316--1385357 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1385306 TTTCTTCGAT
1385316 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
1385335 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
1385355 ATT
1 ATT
1385358 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:1385468 original size:120 final size:119
Alignment explanation
Indices: 1385236--1385461 Score: 280
Period size: 120 Copynumber: 1.9 Consensus size: 119
1385226 ATATTAATTT
* * *
1385236 ATTTATAAATAAAATATTTATTTATTTAGAAAAATCAGAAAATGACTTCTAGGTGCCTTAAGACA
1 ATTTATAAATAAAATATTTATTTATTTAGAAAAATCAAAAAATGACATCCAGGTGCCTTAAGACA
* *
1385301 ACTCTTTTCTTCGATATTAAAAAATAAATAAATAATTAAAACAATTAATATATA
66 ACTCCTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACAATTAATATATA
** * **
1385355 ATTTATAAAATAGGATATTTATTTATTTA-AAAATATCAAAAAATGGACATCCAGTTGTTTTAAG
1 ATTTAT-AAATAAAATATTTATTTATTTAGAAAA-ATCAAAAAAT-GACATCCAGGTGCCTTAAG
** *
1385419 ACTGC-CCTTTCTT-AATATTGAAAAATAAATAAAT-ATTAAAACA
63 ACAACTCCTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACA
1385462 GGATTAAAAT
Statistics
Matches: 91, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
118 9 0.10
119 29 0.32
120 36 0.40
121 17 0.19
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (119 bp):
ATTTATAAATAAAATATTTATTTATTTAGAAAAATCAAAAAATGACATCCAGGTGCCTTAAGACA
ACTCCTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACAATTAATATATA
Found at i:1386823 original size:3 final size:3
Alignment explanation
Indices: 1386809--1386895 Score: 99
Period size: 3 Copynumber: 29.7 Consensus size: 3
1386799 TAAAATTATT
* * * * *
1386809 TAA TAA TTA TAA TAA T-A TAA TAA TTA TAA TTA TAA TTA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1386856 TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
1386896 TTCAAATGAA
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
2 6 0.09
3 62 0.89
4 2 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:1387495 original size:113 final size:112
Alignment explanation
Indices: 1387242--1387897 Score: 915
Period size: 113 Copynumber: 5.8 Consensus size: 112
1387232 TAGAGTTATG
* * *
1387242 CAAAAGGTTGAACAAGTTCTTTTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
** * * *
1387307 TTATGAACACTTCTGGCAATGCTGATCCATCAAATGATGAATTCAAA
66 TTATGAACTTTTCTGGAAAAGTTGATCCATCAAATGATGAATTCAAA
*
1387354 CAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * ** *
1387419 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTTT-TCTGGAAAAGTTGATCCATCAAATGATGAATTCAAA
** * *
1387467 CAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATAAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
1387532 TTATGAAC-TTTCTGGCAATA-TTGATCCATCAAATGATGAATTCAAA
66 TTATGAACTTTTCTGG-AAAAGTTGATCCATCAAATGATGAATTCAAA
* *
1387578 CAAAAGGTTGAAAAAATTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * ** *
1387643 TTATGAACTTTCTCTAGAAAAGTTGATCCATCGAGTGATGGATTTGAG
66 TTATGAACTTT-TCTGGAAAAGTTGATCCATCAAATGATGAATTCAAA
* *
1387691 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTATTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
1387756 TTATAAAC-TTTCTGGCAATA-TTGATCCATCAAATGATGAATTCAAA
66 TTATGAACTTTTCTGG-AAAAGTTGATCCATCAAATGATGAATTCAAA
* *
1387802 CAAAAGGTTGAACAAATTCTTCTCATTATAAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
1387867 TTATGAACTTTCTCTGGAAAAGATGATCCAT
66 TTATGAACTTT-TCTGGAAAAGTTGATCCAT
1387898 TGAGTGATGG
Statistics
Matches: 476, Mismatches: 59, Indels: 17
0.86 0.11 0.03
Matches are distributed among these distances:
111 184 0.39
112 90 0.19
113 202 0.42
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (112 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTTCTGGAAAAGTTGATCCATCAAATGATGAATTCAAA
Found at i:1387632 original size:224 final size:224
Alignment explanation
Indices: 1387241--1387913 Score: 1148
Period size: 224 Copynumber: 3.0 Consensus size: 224
1387231 ATAGAGTTAT
* * *
1387241 GCAAAAGGTTGAACAAGTTCTTTTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTC
* **
1387306 ATTATGAACACTTCTGGCAATGCTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAAT
66 ATTATGAAC-TTTCTGGCAATATTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAAT
* *
1387371 TCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
130 TCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* *
1387436 AAAAGCTGATCCATCAAGTGATGGATTTGA
195 AAAAGATGATCCATCGAGTGATGGATTTGA
* *
1387466 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATAAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTC
*
1387531 ATTATGAACTTTCTGGCAATATTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAAAAAATT
66 ATTATGAACTTTCTGGCAATATTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATT
* *
1387596 CTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTAGA
131 CTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
*
1387661 AAAGTTGATCCATCGAGTGATGGATTTGA
196 AAAGATGATCCATCGAGTGATGGATTTGA
* *
1387690 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTATTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTC
*
1387755 ATTATAAACTTTCTGGCAATATTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATT
66 ATTATGAACTTTCTGGCAATATTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATT
*
1387820 CTTCTCATTATAAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
131 CTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
*
1387885 AAAGATGATCCATTGAGTGATGGATTTGA
196 AAAGATGATCCATCGAGTGATGGATTTGA
1387914 ATCTTTGCTA
Statistics
Matches: 423, Mismatches: 25, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
224 354 0.84
225 69 0.16
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (224 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTC
ATTATGAACTTTCTGGCAATATTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATT
CTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
AAAGATGATCCATCGAGTGATGGATTTGA
Found at i:1399904 original size:66 final size:66
Alignment explanation
Indices: 1399798--1399979 Score: 355
Period size: 66 Copynumber: 2.8 Consensus size: 66
1399788 TTCTCTATGC
1399798 CTGACACGGAGAATAAATTCTCACGAAGACATAGAGCATATGAACCACGAAAGTTACTTGCTAGG
1 CTGACACGGAGAATAAATTCTCACGAAGACATAGAGCATATGAACCACGAAAGTTACTTGCTAGG
1399863 T
66 T
*
1399864 CTGACACGGAGAATAAATTCTCACGAATACATAGAGCATATGAACCACGAAAGTTACTTGCTAGG
1 CTGACACGGAGAATAAATTCTCACGAAGACATAGAGCATATGAACCACGAAAGTTACTTGCTAGG
1399929 T
66 T
1399930 CTGACACGGAGAATAAATTCTCACGAAGACATAGAGCATATGAACCACGA
1 CTGACACGGAGAATAAATTCTCACGAAGACATAGAGCATATGAACCACGA
1399980 CAGCTTGGCG
Statistics
Matches: 114, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 114 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (66 bp):
CTGACACGGAGAATAAATTCTCACGAAGACATAGAGCATATGAACCACGAAAGTTACTTGCTAGG
T
Found at i:1400602 original size:23 final size:24
Alignment explanation
Indices: 1400576--1400630 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
1400566 AAAATTATAA
*
1400576 TTATGAAA-AATATATTAATTTAT
1 TTATGAAATAAAATATTAATTTAT
*
1400599 TTAT-AAATAAAATATTTATTTAT
1 TTATGAAATAAAATATTAATTTAT
1400622 TTA-GAAATA
1 TTATGAAATA
1400631 TCAGAAAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 3 0.11
23 25 0.89
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (24 bp):
TTATGAAATAAAATATTAATTTAT
Found at i:1400825 original size:116 final size:115
Alignment explanation
Indices: 1400605--1400818 Score: 272
Period size: 116 Copynumber: 1.9 Consensus size: 115
1400595 TTATTTATAA
* * * * *
1400605 ATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGGTGCCTTAAGACAACTCTTTT
1 ATAAAATATATATTTATTTAAAAATATCAGAAAAGGACATCCAGGTGCCTTAAGACAACTCCTTT
* *
1400670 CTTCGATATTAAAAAATAAATAATTAATTAAAACAATTAATATATAATTT
66 CTTCAATATTAAAAAATAAATAAATAATTAAAACAATTAATATATAATTT
* ** **
1400720 ATAAAATATGATATTTATTTAAAAATATCAGAAAATGGACATCCAGTTGTTTTAAGACTGC-CCT
1 ATAAAATAT-ATATTTATTTAAAAATATCAGAAAA-GGACATCCAGGTGCCTTAAGACAACTCCT
*
1400784 TTCTT-AATATTGAAAAATAAATAAAT-ATTAAAACA
64 TTCTTCAATATTAAAAAATAAATAAATAATTAAAACA
1400819 GGATTAAAAT
Statistics
Matches: 84, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
114 9 0.11
115 27 0.32
116 30 0.36
117 18 0.21
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (115 bp):
ATAAAATATATATTTATTTAAAAATATCAGAAAAGGACATCCAGGTGCCTTAAGACAACTCCTTT
CTTCAATATTAAAAAATAAATAAATAATTAAAACAATTAATATATAATTT
Found at i:1402254 original size:3 final size:3
Alignment explanation
Indices: 1402246--1402314 Score: 72
Period size: 3 Copynumber: 23.7 Consensus size: 3
1402236 TAAAATTATT
* * * *
1402246 TAA TAA TAA TAA TAA T-A TAA TAA TTA TAA TTA TAA TTA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1402293 TAA TAA TAA -AA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA T-AA TAA TA
1402315 TTCAAATGAA
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
2 6 0.11
3 48 0.86
4 2 0.04
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:1403742 original size:20 final size:20
Alignment explanation
Indices: 1403717--1403765 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1403707 CGAAACTTAA
1403717 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
1403737 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1403757 ATCGCAACG
1 ATCGCAACG
1403766 GGATAATCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1403866 original size:20 final size:20
Alignment explanation
Indices: 1403841--1403909 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
1403831 GCGATTATCC
*
1403841 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
1403861 CGTTGCGATAGTC-ATTTCCG
1 CGTTGCGATAGTCAATTT-CG
* * *
1403881 TGTTGAGATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
1403901 CGTTGCGAT
1 CGTTGCGAT
1403910 TTAAGTTTCG
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 3 0.07
20 35 0.85
21 3 0.07
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:1403924 original size:19 final size:20
Alignment explanation
Indices: 1403896--1403938 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
1403886 AGATAGTCAT
1403896 TTTCGCGTTGCGA-TTTAAG
1 TTTCGCGTTGCGATTTTAAG
*
1403915 TTTCGTGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
1403935 TTTC
1 TTTC
1403939 AGAAACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.49
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTAAG
Found at i:1404499 original size:21 final size:21
Alignment explanation
Indices: 1404475--1404527 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
1404465 CCTCAAGAGT
*
1404475 CCCCTCCCACCGTTTAAAAGG
1 CCCCTCCCACCGTTGAAAAGG
** * *
1404496 CCCCTGTCATCGTTGAAGAGG
1 CCCCTCCCACCGTTGAAAAGG
*
1404517 TCCCTCCCACC
1 CCCCTCCCACC
1404528 ATTCAAGAGC
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.19, C:0.43, G:0.17, T:0.21
Consensus pattern (21 bp):
CCCCTCCCACCGTTGAAAAGG
Found at i:1404515 original size:42 final size:42
Alignment explanation
Indices: 1404414--1404533 Score: 116
Period size: 42 Copynumber: 2.9 Consensus size: 42
1404404 GCCCGACTCA
* * * * * *
1404414 CCTGTCATCGTTCAAGAGGCCTCACCTATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAAAGGCC
* ** *
1404456 CCTATCATCCCTCAAGAGTCCCCTCCCACCGTTTAAAAGGCC
1 CCTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAAAGGCC
* *
1404498 CCTGTCATCGTTGAAGAGGT-CCCTCCCACCATTCAA
1 CCTGTCATCGTTCAAGA-GTCCCCTCCCACCGTTCAA
1404534 GAGCCCGATT
Statistics
Matches: 61, Mismatches: 16, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
42 59 0.97
43 2 0.03
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.23
Consensus pattern (42 bp):
CCTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAAAGGCC
Found at i:1405931 original size:14 final size:14
Alignment explanation
Indices: 1405912--1405973 Score: 70
Period size: 14 Copynumber: 4.3 Consensus size: 14
1405902 TTGCTTGTTT
1405912 AATTGATTTGTAAA
1 AATTGATTTGTAAA
1405926 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
1405940 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
1405955 TATTGATGTGTAAA
1 AATTGATTTGTAAA
1405969 TAATT
1 -AATT
1405974 CTTATTTGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
14 26 0.67
15 13 0.33
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1405946 original size:28 final size:29
Alignment explanation
Indices: 1405914--1405968 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
1405904 GCTTGTTTAA
*
1405914 TTGATTTG-TAAAAATTGATTTGTAAAAG
1 TTGATTTGTTAAAAATTGATGTGTAAAAG
* *
1405942 TTGATTTGTTTAATATTGATGTGTAAA
1 TTGATTTGTTAAAAATTGATGTGTAAA
1405969 TAATTCTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (29 bp):
TTGATTTGTTAAAAATTGATGTGTAAAAG
Found at i:1406113 original size:20 final size:20
Alignment explanation
Indices: 1406088--1406145 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
1406078 CGCTAAATTC
1406088 AAAATCGCAATGCGAAAGCA
1 AAAATCGCAATGCGAAAGCA
1406108 AAAATCGCAATGCGAAAGCA
1 AAAATCGCAATGCGAAAGCA
*
1406128 AAAATCGCAACGCGAAAG
1 AAAATCGCAATGCGAAAG
1406146 TCAATTTGCG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.50, C:0.21, G:0.21, T:0.09
Consensus pattern (20 bp):
AAAATCGCAATGCGAAAGCA
Found at i:1406197 original size:34 final size:34
Alignment explanation
Indices: 1406154--1406295 Score: 149
Period size: 34 Copynumber: 4.0 Consensus size: 34
1406144 AGTCAATTTG
* * *
1406154 CGTTGCGATAGTCTAATACGCTTTGCGATTTTCT
1 CGTTGCGATAGTCAAATACGCGTTGCGATTTTCA
*
1406188 CGTTGCGATAGTCAAATACCCGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATACGCGTTGCGAT--T----TTCA
* *
1406228 CGTTGCGATAGTCAAATTCGCGTTGTGATTTTCA
1 CGTTGCGATAGTCAAATACGCGTTGCGATTTTCA
* * *
1406262 CGTTGCGATAGTCAAATTCGCGTTGTGATATTCA
1 CGTTGCGATAGTCAAATACGCGTTGCGATTTTCA
1406296 AATGAATGTG
Statistics
Matches: 94, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
34 63 0.67
36 1 0.01
38 1 0.01
40 29 0.31
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATACGCGTTGCGATTTTCA
Found at i:1406238 original size:74 final size:74
Alignment explanation
Indices: 1406154--1406298 Score: 209
Period size: 74 Copynumber: 2.0 Consensus size: 74
1406144 AGTCAATTTG
* * *
1406154 CGTTGCGATAGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTTGCGATAA
1 CGTTGCGATAGTCAAATACGCGTTGCGATTTTCACGTTGCGATAGTCAAATACCCGTTGCGATAA
1406219 TCAAATTCA
66 TCAAATTCA
* * * * * *
1406228 CGTTGCGATAGTCAAATTCGCGTTGTGATTTTCACGTTGCGATAGTCAAATTCGCGTTGTGATAT
1 CGTTGCGATAGTCAAATACGCGTTGCGATTTTCACGTTGCGATAGTCAAATACCCGTTGCGATAA
1406293 TCAAAT
66 TCAAAT
1406299 GAATGTGTAA
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
74 62 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (74 bp):
CGTTGCGATAGTCAAATACGCGTTGCGATTTTCACGTTGCGATAGTCAAATACCCGTTGCGATAA
TCAAATTCA
Found at i:1406245 original size:20 final size:20
Alignment explanation
Indices: 1406188--1406298 Score: 108
Period size: 20 Copynumber: 5.8 Consensus size: 20
1406178 GCGATTTTCT
* *
1406188 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCA
*
1406208 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCA
*
1406228 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCA
*
1406248 CGTTGTGAT--T----TTCA
1 CGTTGCGATAGTCAAATTCA
*
1406262 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCA
* *
1406282 CGTTGTGATATTCAAAT
1 CGTTGCGATAGTCAAAT
1406299 GAATGTGTAA
Statistics
Matches: 74, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
14 11 0.15
16 1 0.01
18 1 0.01
20 61 0.82
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCA
Found at i:1406521 original size:140 final size:140
Alignment explanation
Indices: 1406269--1406551 Score: 521
Period size: 140 Copynumber: 2.0 Consensus size: 140
1406259 TCACGTTGCG
*
1406269 ATAGTCAAATTCGCGTTGTGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
*
1406334 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCATAACTGAAAATGTTAAAAGTTTACACATAA
1406399 AATACACATA
131 AATACACATA
* *
1406409 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAATAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
*
1406474 TAGCAATGTTCAAACTCAAGTTACTAATACATGCATAACTGAAAATGTTAAAATTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCATAACTGAAAATGTTAAAAGTTTACACATAA
1406539 AATACACATA
131 AATACACATA
1406549 ATA
1 ATA
1406552 CAACGTTTGC
Statistics
Matches: 138, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 138 1.00
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCATAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:1408940 original size:24 final size:24
Alignment explanation
Indices: 1408906--1408959 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1408896 CTAAAACATC
*
1408906 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACAAAG
* *
1408930 ATCAAAGTCCGGGTATTGACAAAG
1 ATCAAAATCCGAGTATTGACAAAG
1408954 ATCAAA
1 ATCAAA
1408960 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACAAAG
Found at i:1409803 original size:20 final size:20
Alignment explanation
Indices: 1409780--1409868 Score: 108
Period size: 20 Copynumber: 4.4 Consensus size: 20
1409770 GAAATTCAGT
* *
1409780 GTTGCGACAGTCAGAATCGT
1 GTTGCGATAGTCAGAATCGC
*
1409800 GTTGCGATAGTCAAAATCGC
1 GTTGCGATAGTCAGAATCGC
**
1409820 GTTGCGATTATGT-ATTATCGC
1 GTTGCGA-TA-GTCAGAATCGC
1409841 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
1409861 GTTGCGAT
1 GTTGCGAT
1409869 TTACATATTC
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.03
20 40 0.68
21 15 0.25
22 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:1409845 original size:41 final size:39
Alignment explanation
Indices: 1409795--1409907 Score: 136
Period size: 41 Copynumber: 2.8 Consensus size: 39
1409785 GACAGTCAGA
* **
1409795 ATCGTGTTGCGATAGTCAAAATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGATAGTCAAAATCGCGTTGCGATT-TACA-T
*
1409836 ATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTTACAT
1 ATCGCGTTGCGATAGTCAAAATCGCGTTGCGATTTACAT
* * *
1409875 ATTCGCATTGTGATGGTCAAAATCGCGTTGCGA
1 A-TCGCGTTGCGATAGTCAAAATCGCGTTGCGA
1409908 ATCTGGAAAC
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
39 2 0.03
40 29 0.46
41 32 0.51
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.33
Consensus pattern (39 bp):
ATCGCGTTGCGATAGTCAAAATCGCGTTGCGATTTACAT
Found at i:1409957 original size:19 final size:19
Alignment explanation
Indices: 1409933--1409969 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1409923 TGCGATACTG
* *
1409933 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTACGATTTA
1409952 GAGATCGCATTACGATTT
1 GAGATCGCATTACGATTT
1409970 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTACGATTTA
Found at i:1411041 original size:16 final size:18
Alignment explanation
Indices: 1411009--1411041 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1410999 ATCACAAAAA
1411009 TTTGATTTTTATGAATAT
1 TTTGATTTTTATGAATAT
1411027 TTTG-TTTTTAT-AATA
1 TTTGATTTTTATGAATA
1411042 ATTATTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (18 bp):
TTTGATTTTTATGAATAT
Found at i:1412083 original size:180 final size:176
Alignment explanation
Indices: 1411818--1412349 Score: 453
Period size: 180 Copynumber: 2.9 Consensus size: 176
1411808 ATATATGCTA
* ** * * * *
1411818 TCACTATAGTTAAAATTTATAACTACAAATATAATTTGTCACAAAAACGTGAATATCATTATTTT
1 TCACTATAATTAAAACATATAACGACAAACAAAATTTGTCACAAAAACTTGAATATCATTA--TT
* * * ** *
1411883 TTTTATGACAATGATTTTGTAATAATTATTAACACTTATAGTTACAAAATTTGTCACTATATGAC
64 TGTTGTGATAATTTTTTTGTAATAATTATTAA-ACTTATAGTTACAAAACTTGTCACTATATGAC
1411948 TTTTTTGGCCAAAAAAATATGGAGGGAAATATTTGTGACAATATATTTTG
128 TTTTTTGGCCAAAAAAAT-TGGAGGGAAATATTTGTGACAATATATTTTG
* * *** * * *
1411998 TCAGTATAATTAAAACATATAACGACAAATATTGTTTTTTTATTAAAAACTTGAATATCATTATT
1 TCACTATAATTAAAACATATAACGACAAACA-AAATTTGTCA-CAAAAACTTGAATATCATTATT
* * *
1412063 TGTTGTGATAATTTTTTTGTAATAATAATTATAGCTTATAGTTACAAAACTTGTCACTATATGAT
64 TGTTGTGATAATTTTTTTGTAATAATTATTA-AACTTATAGTTACAAAACTTGTCACTATATGAC
**** * * *
1412128 TTTGTTTTTTTACCAAAAATTGGA--GATAATCATTTATGACTATATATTTTG
128 TTT-TTTGGCCA-AAAAAATTGGAGGGA-AAT-ATTTGTGACAATATATTTTG
* ** ** * *
1412179 TCACTATAATTAAAATATATAATTACAAACAAAATTTGTCACAACAAA-TCCAAATCTCATTATC
1 TCACTATAATTAAAACATATAACGACAAACAAAATTTGTCACAA-AAACT-TGAATATCATTATT
* * * * * *
1412243 TGTTGTGATAATTTTTTTGTCATAA-TACTAAAACTTTTAGTTACAAAAGTTGTTACTATATGCC
64 TGTTGTGATAATTTTTTTGTAATAATTA-TTAAACTTATAGTTACAAAACTTGTCACTATATGAC
* *
1412307 TTCAATTTGGTGCC-AAAAAATTGGAGGGAAACATTTGTGACAA
128 TT---TTTTG-GCCAAAAAAATTGGAGGGAAATATTTGTGACAA
1412350 AAAATAGTAA
Statistics
Matches: 276, Mismatches: 60, Indels: 32
0.75 0.16 0.09
Matches are distributed among these distances:
179 35 0.13
180 151 0.55
181 63 0.23
182 27 0.10
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (176 bp):
TCACTATAATTAAAACATATAACGACAAACAAAATTTGTCACAAAAACTTGAATATCATTATTTG
TTGTGATAATTTTTTTGTAATAATTATTAAACTTATAGTTACAAAACTTGTCACTATATGACTTT
TTTGGCCAAAAAAATTGGAGGGAAATATTTGTGACAATATATTTTG
Found at i:1414514 original size:53 final size:53
Alignment explanation
Indices: 1414416--1414519 Score: 138
Period size: 53 Copynumber: 2.0 Consensus size: 53
1414406 AACAACTTTG
* * *
1414416 GGTATTGATACCAAGCCTTCGATATGGATATCGGTTCATCTGGTATAGATATC
1 GGTATGGATACCAAGCCTTCGATATGGATATCAGTTCATCCGGTATAGATATC
* * *
1414469 GGTATGGATACCAATCCTTCGATATGGATA-CTAGTTTATCCGGTATGGATA
1 GGTATGGATACCAAGCCTTCGATATGGATATC-AGTTCATCCGGTATAGATA
1414520 CCAACTGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
52 1 0.02
53 43 0.98
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (53 bp):
GGTATGGATACCAAGCCTTCGATATGGATATCAGTTCATCCGGTATAGATATC
Found at i:1416738 original size:20 final size:20
Alignment explanation
Indices: 1416713--1416781 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
1416703 TTTTTCGACT
*
1416713 ATCGCAATATGAATATGTAA
1 ATCGCAATGTGAATATGTAA
* * *
1416733 ATCGCAATGCGAGTATG-ACT
1 ATCGCAATGTGAATATGTA-A
*
1416753 ATCGCAACGTGAATATGTAA
1 ATCGCAATGTGAATATGTAA
1416773 ATCGCAATG
1 ATCGCAATG
1416782 CGATTATGAC
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
19 1 0.03
20 36 0.95
21 1 0.03
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (20 bp):
ATCGCAATGTGAATATGTAA
Found at i:1416789 original size:20 final size:20
Alignment explanation
Indices: 1416713--1416789 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 20
1416703 TTTTTCGACT
**
1416713 ATCGCAATATGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* *
1416733 ATCGCAATGCGAGTATG-ACT
1 ATCGCAATGCGAATATGTA-A
* *
1416753 ATCGCAACGTGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
1416773 ATCGCAATGCGATTATG
1 ATCGCAATGCGAATATG
1416790 ACTATCGCAA
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
19 1 0.02
20 42 0.95
21 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:1416796 original size:20 final size:20
Alignment explanation
Indices: 1416733--1416822 Score: 85
Period size: 20 Copynumber: 4.5 Consensus size: 20
1416723 GAATATGTAA
*
1416733 ATCGCAATGCGAGTATGACT
1 ATCGCAATGCGATTATGACT
* * * *
1416753 ATCGCAACGTGAATATGTA-A
1 ATCGCAATGCGATTATG-ACT
1416773 ATCGCAATGCGATTATGACT
1 ATCGCAATGCGATTATGACT
*
1416793 ATCGCAACT-CGATTCTGACT
1 ATCGCAA-TGCGATTATGACT
*
1416813 GTCGCAATGC
1 ATCGCAATGC
1416823 TGAATTTCAA
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
19 2 0.04
20 52 0.93
21 2 0.04
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (20 bp):
ATCGCAATGCGATTATGACT
Found at i:1416822 original size:40 final size:40
Alignment explanation
Indices: 1416709--1416800 Score: 157
Period size: 40 Copynumber: 2.3 Consensus size: 40
1416699 GCAATTTTTC
**
1416709 GACTATCGCAATATGAATATGTAAATCGCAATGCGAGTAT
1 GACTATCGCAACGTGAATATGTAAATCGCAATGCGAGTAT
*
1416749 GACTATCGCAACGTGAATATGTAAATCGCAATGCGATTAT
1 GACTATCGCAACGTGAATATGTAAATCGCAATGCGAGTAT
1416789 GACTATCGCAAC
1 GACTATCGCAAC
1416801 TCGATTCTGA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (40 bp):
GACTATCGCAACGTGAATATGTAAATCGCAATGCGAGTAT
Found at i:1417692 original size:24 final size:24
Alignment explanation
Indices: 1417641--1417694 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1417631 GTATTCAAAA
*
1417641 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGAAC
* *
1417665 TTTGATCTTGGTCAATACTCGAAT
1 TTTGATCTTGGTCAATACCCGAAC
1417689 TTTGAT
1 TTTGAT
1417695 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGAAC
Found at i:1419958 original size:12 final size:12
Alignment explanation
Indices: 1419941--1419971 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1419931 CAAGTAAAAG
1419941 GCAATCAAAATC
1 GCAATCAAAATC
1419953 GCAATCAAAATC
1 GCAATCAAAATC
*
1419965 TCAATCA
1 GCAATCA
1419972 CAACCGGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.48, C:0.26, G:0.06, T:0.19
Consensus pattern (12 bp):
GCAATCAAAATC
Found at i:1420174 original size:20 final size:20
Alignment explanation
Indices: 1420149--1420429 Score: 291
Period size: 20 Copynumber: 14.7 Consensus size: 20
1420139 CACATTCATT
1420149 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
1420169 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
* * *
1420189 TGACTATCACAACGTGAATT
1 TGACTATCGCAACGCGAATA
* *
1420209 TGAATATCGCAACG-G--GA
1 TGACTATCGCAACGCGAATA
* *
1420226 T-A--ATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
*
1420243 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
*
1420263 TGACTATCGCAACG-G--GA
1 TGACTATCGCAACGCGAATA
* *
1420280 T-A--ATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
*
1420297 TGACTATCGCAACGCGAAAA
1 TGACTATCGCAACGCGAATA
*
1420317 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
* * *
1420337 TAACTATCGCAACACGAATT
1 TGACTATCGCAACGCGAATA
1420357 TGACTATCGCAACGCGAA-A
1 TGACTATCGCAACGCGAATA
*
1420376 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
* * *
1420396 TGATTATCGCAACGGGAATT
1 TGACTATCGCAACGCGAATA
1420416 TGACTATCGCAACG
1 TGACTATCGCAACG
1420430 AGAAAATCGC
Statistics
Matches: 220, Mismatches: 28, Indels: 26
0.80 0.10 0.09
Matches are distributed among these distances:
14 16 0.07
15 2 0.01
16 2 0.01
17 6 0.03
18 2 0.01
19 20 0.09
20 172 0.78
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (20 bp):
TGACTATCGCAACGCGAATA
Found at i:1420256 original size:54 final size:54
Alignment explanation
Indices: 1420174--1420389 Score: 254
Period size: 54 Copynumber: 3.9 Consensus size: 54
1420164 GAATATGACT
* * * * *
1420174 ATCGCAACGCGAATATGACTATCACAACGTGAATTTGAATATCGCAACGGGATA
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATA
1420228 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATA
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATA
** *
1420282 ATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGCGAATTTAA
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACG-GGA--T-A
** ** *
1420340 CTATCGCAACACGAATTTGACTATCGCAACGCGAA-ATGACTATCGCAACG
1 --ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACG
1420390 CGAATTTGAT
Statistics
Matches: 144, Mismatches: 12, Indels: 7
0.88 0.07 0.04
Matches are distributed among these distances:
54 96 0.67
55 2 0.01
57 1 0.01
58 1 0.01
59 15 0.10
60 29 0.20
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (54 bp):
ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATA
Found at i:1420276 original size:74 final size:74
Alignment explanation
Indices: 1420154--1420429 Score: 279
Period size: 74 Copynumber: 3.7 Consensus size: 74
1420144 TCATTTGACT
* * * *
1420154 ATCGCAACGCGAATATGACTATCGCAACGCGAATATGACTATCACAACGTGAATTTGAATATCGC
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGAATATCGC
1420219 AACGGGATA
66 AACGGGATA
* * * * *
1420228 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCA-AT-G
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGCGA-ATTTGAATATCG
***
1420291 CGAAAATGACT-
65 C-AACGGGA-TA
* * *
1420302 ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTAACTATCGCAACACGAATTTGACTATCGC
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGAATATCGC
*
1420367 AACGCGAAATGA
66 AACG-G-GAT-A
** * *
1420379 CTATCGCAACGCGAATTTGATTATCGCAACGGGAATTTGACTATCGCAACG
1 --ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACG
1420430 AGAAAATCGC
Statistics
Matches: 162, Mismatches: 29, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
73 5 0.03
74 105 0.65
75 8 0.05
76 1 0.01
79 43 0.27
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (74 bp):
ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGAATATCGC
AACGGGATA
Found at i:1420604 original size:36 final size:34
Alignment explanation
Indices: 1420564--1420643 Score: 114
Period size: 30 Copynumber: 2.4 Consensus size: 34
1420554 TCAACTTTTA
1420564 ATCAATTAAACAAGCACAAATAAGAATTATTTACAC
1 ATCAATTAAACAA--ACAAATAAGAATTATTTACAC
1420600 ATCAATT----AAACAAATAAGAATTATTTACAC
1 ATCAATTAAACAAACAAATAAGAATTATTTACAC
1420630 ATCAATTAAACAAA
1 ATCAATTAAACAAA
1420644 TCAACTCTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
30 28 0.70
32 2 0.05
34 3 0.08
36 7 0.17
ACGTcount: A:0.55, C:0.15, G:0.04, T:0.26
Consensus pattern (34 bp):
ATCAATTAAACAAACAAATAAGAATTATTTACAC
Found at i:1420613 original size:30 final size:30
Alignment explanation
Indices: 1420579--1420644 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
1420569 TTAAACAAGC
1420579 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
1420609 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
1420639 ACAAAT
1 ACAAAT
1420645 CAACTCTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.55, C:0.14, G:0.03, T:0.29
Consensus pattern (30 bp):
ACAAATAAGAATTATTTACACATCAATTAA
Found at i:1422659 original size:20 final size:20
Alignment explanation
Indices: 1422634--1422709 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
1422624 TCGCAACACG
*
1422634 AATGACTATCGCAACGTGAA
1 AATGACTATCGCAACGCGAA
1422654 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
*
1422674 AATGACTATCGCAACGCGAT
1 AATGACTATCGCAACGCGAA
**
1422694 TTTGACTATCGCAACG
1 AATGACTATCGCAACG
1422710 AGAGAATTGC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.21
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:1422826 original size:20 final size:20
Alignment explanation
Indices: 1422752--1422876 Score: 137
Period size: 20 Copynumber: 6.2 Consensus size: 20
1422742 ACGATTCTCT
*
1422752 CGTTGCGATAGTCAAATT-CG
1 CGTTGCGATAGTC-ATTTCCG
* * *
1422772 CATTGTGATAGTCAAATT-CG
1 CGTTGCGATAGTC-ATTTCCG
* *
1422792 CGTTGTGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
1422812 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
1422832 CGTTGCGAAAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
1422852 CGTTGCAAAAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
1422872 CGTTG
1 CGTTG
1422877 AGAAAGTAAA
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
19 3 0.03
20 93 0.97
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:1423050 original size:18 final size:18
Alignment explanation
Indices: 1423027--1423076 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
1423017 TTTACTAAGC
1423027 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
1423045 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
1423063 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
1423077 TACGAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:1424872 original size:20 final size:20
Alignment explanation
Indices: 1424814--1424887 Score: 94
Period size: 20 Copynumber: 3.7 Consensus size: 20
1424804 GAAACTTAAA
* **
1424814 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
*
1424834 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
1424854 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1424874 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1424888 CTAAAATCAC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1425311 original size:22 final size:22
Alignment explanation
Indices: 1425280--1425336 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
1425270 GATGGAGATA
1425280 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
1425302 GACTGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1425324 GACGGATGTCGCC
1 GACGGATTTCGCC
1425337 TTAGAGAGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.18, C:0.19, G:0.42, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1425525 original size:20 final size:20
Alignment explanation
Indices: 1425500--1425637 Score: 111
Period size: 20 Copynumber: 6.9 Consensus size: 20
1425490 GCGCTTTAAA
* *
1425500 AATCGCATTGCGACAGTTAG
1 AATCGCATTGCGATAGTCAG
*
1425520 AATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
*
1425540 AATCGCATTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAG
* * *
1425560 AATCGCGTTGCGAT-TTACAT
1 AATCGCATTGCGATAGT-CAG
* * *
1425580 ATTCGCGTTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAG
* *
1425600 ACA-CGCATTGCGAT-TTACAT
1 A-ATCGCATTGCGATAGT-CAG
*
1425620 ATTCGCATTGCGATAGTC
1 AATCGCATTGCGATAGTC
1425638 GGAAAATCGC
Statistics
Matches: 98, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
19 2 0.02
20 94 0.96
21 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.30
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAG
Found at i:1425564 original size:40 final size:40
Alignment explanation
Indices: 1425500--1425637 Score: 163
Period size: 40 Copynumber: 3.5 Consensus size: 40
1425490 GCGCTTTAAA
* * * * *
1425500 AATCGCATTGCGACAGTTAGAATCGCGTTGCGATAGT-CAG
1 AATCGCATTGCGATAGTCATAATCGCGTTGCGAT-TTACAT
1425540 AATCGCATTGCGATAGTCATAATCGCGTTGCGATTTACAT
1 AATCGCATTGCGATAGTCATAATCGCGTTGCGATTTACAT
* * *
1425580 ATTCGCGTTGCGATAGTCATACA-CGCATTGCGATTTACAT
1 AATCGCATTGCGATAGTCATA-ATCGCGTTGCGATTTACAT
*
1425620 ATTCGCATTGCGATAGTC
1 AATCGCATTGCGATAGTC
1425638 GGAAAATCGC
Statistics
Matches: 87, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
39 1 0.01
40 85 0.98
41 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.30
Consensus pattern (40 bp):
AATCGCATTGCGATAGTCATAATCGCGTTGCGATTTACAT
Found at i:1436508 original size:14 final size:14
Alignment explanation
Indices: 1436486--1436559 Score: 103
Period size: 14 Copynumber: 5.2 Consensus size: 14
1436476 GTAATTTGTT
1436486 TTATGGAAATTGAA
1 TTATGGAAATTGAA
* *
1436500 TTCTGGAAAATGAA
1 TTATGGAAATTGAA
*
1436514 TTACTGTAAATTGAA
1 TTA-TGGAAATTGAA
1436529 TTATGGAAATTGAA
1 TTATGGAAATTGAA
*
1436543 TTATGGAAAATGAA
1 TTATGGAAATTGAA
1436557 TTA
1 TTA
1436560 CATTTATGGA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
14 40 0.77
15 12 0.23
ACGTcount: A:0.43, C:0.03, G:0.19, T:0.35
Consensus pattern (14 bp):
TTATGGAAATTGAA
Found at i:1436535 original size:29 final size:28
Alignment explanation
Indices: 1436486--1436559 Score: 103
Period size: 29 Copynumber: 2.6 Consensus size: 28
1436476 GTAATTTGTT
*
1436486 TTATGGAAATTGAATTCTGGAAAATGAA
1 TTATGGAAATTGAATTATGGAAAATGAA
* *
1436514 TTACTGTAAATTGAATTATGGAAATTGAA
1 TTA-TGGAAATTGAATTATGGAAAATGAA
*
1436543 TTATGGAAAATGAATTA
1 TTATGGAAATTGAATTA
1436560 CATTTATGGA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
28 15 0.38
29 25 0.62
ACGTcount: A:0.43, C:0.03, G:0.19, T:0.35
Consensus pattern (28 bp):
TTATGGAAATTGAATTATGGAAAATGAA
Found at i:1436956 original size:23 final size:23
Alignment explanation
Indices: 1436907--1436957 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1436897 GTGTTAAATT
**
1436907 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
1436930 ATATTTTAAACATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
1436953 ATATT
1 ATATT
1436958 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:1437009 original size:19 final size:19
Alignment explanation
Indices: 1436945--1437011 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
1436935 TTAAACATCT
1436945 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
* *
1436964 TTATT-ATATTAATATTAA
1 TTATTAATAATATTATTAA
* * *
1436982 ATATAAATAATATTATTCA
1 TTATTAATAATATTATTAA
1437001 TTATTAATAAT
1 TTATTAATAAT
1437012 TTAATATTAT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
18 5 0.14
19 32 0.86
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:1437084 original size:25 final size:25
Alignment explanation
Indices: 1437056--1437103 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
1437046 AAATTTTATT
1437056 AATAAT-TTATTATTATTAAAATAAA
1 AATAATCTTA-TATTATTAAAATAAA
*
1437081 AATAATCTTATATTATTATAATA
1 AATAATCTTATATTATTAAAATA
1437104 TAATTGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
AATAATCTTATATTATTAAAATAAA
Found at i:1437836 original size:24 final size:24
Alignment explanation
Indices: 1437797--1437860 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
1437787 TCGTTCGTTA
* *
1437797 AAATGATAAACGAACAGAAACAAAC
1 AAATG-TAAACAAACACAAACAAAC
*
1437822 AAACT-TAAACAAACACAAACGAAC
1 AAA-TGTAAACAAACACAAACAAAC
*
1437846 GAATGTAAACAAACA
1 AAATGTAAACAAACA
1437861 TAAAATTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
23 1 0.03
24 28 0.85
25 3 0.09
26 1 0.03
ACGTcount: A:0.62, C:0.19, G:0.09, T:0.09
Consensus pattern (24 bp):
AAATGTAAACAAACACAAACAAAC
Found at i:1438782 original size:31 final size:31
Alignment explanation
Indices: 1438725--1438839 Score: 96
Period size: 31 Copynumber: 3.7 Consensus size: 31
1438715 ATTTAAATAA
*
1438725 AAAAATAAATATTTT-AGATACCTATTTTGATC
1 AAAAA-AAATATTTTAAG-TACTTATTTTGATC
*
1438757 AAAAAAAATATTTTAAGTACTTATTTT-AAC
1 AAAAAAAATATTTTAAGTACTTATTTTGATC
* * * * *
1438787 AAAATAGATAACTTTAAATACTTACTTTGAGT-
1 AAAAAAAAT-ATTTTAAGTACTTATTTTGA-TC
1438819 --AAAAAATATTTTAAGTACTTA
1 AAAAAAAATATTTTAAGTACTTA
1438840 AATGAAAAAT
Statistics
Matches: 67, Mismatches: 12, Indels: 11
0.74 0.13 0.12
Matches are distributed among these distances:
29 12 0.18
30 14 0.21
31 33 0.49
32 8 0.12
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (31 bp):
AAAAAAAATATTTTAAGTACTTATTTTGATC
Found at i:1443690 original size:12 final size:12
Alignment explanation
Indices: 1443670--1443704 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
1443660 GATTTCAGGA
1443670 CTTTCCCCCCTC
1 CTTTCCCCCCTC
*
1443682 CTTTTCCCCCTC
1 CTTTCCCCCCTC
1443694 CTTTCCCCCCT
1 CTTTCCCCCCT
1443705 TACCCTATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (12 bp):
CTTTCCCCCCTC
Found at i:1450527 original size:25 final size:25
Alignment explanation
Indices: 1450493--1450553 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 25
1450483 GTTGTGTGGT
*
1450493 ATGTGATATGTCATCAG-TTTGGGTG
1 ATGTGATATGTCAT-AGTTTTAGGTG
*
1450518 ATGTGATATGTCATTGTTTTAGGTG
1 ATGTGATATGTCATAGTTTTAGGTG
1450543 ATGTGATATGT
1 ATGTGATATGT
1450554 TACTTGAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 1 0.03
25 32 0.97
ACGTcount: A:0.21, C:0.05, G:0.30, T:0.44
Consensus pattern (25 bp):
ATGTGATATGTCATAGTTTTAGGTG
Found at i:1453561 original size:19 final size:19
Alignment explanation
Indices: 1453525--1453561 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1453515 TGAAAATGAT
*
1453525 TTGATTTTGAAAGCCAAAG
1 TTGATTTTGAAAACCAAAG
*
1453544 TTGATTTTGAAAATCAAA
1 TTGATTTTGAAAACCAAA
1453562 ATGAAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (19 bp):
TTGATTTTGAAAACCAAAG
Found at i:1454976 original size:23 final size:23
Alignment explanation
Indices: 1454931--1454992 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1454921 CGGTAAAGCG
*
1454931 CTACCGGTTTTGTTA-TTTTTTT
1 CTACCGATTTTGTTATTTTTTTT
1454953 CTACCGATTTTGTTATTTTTTTT
1 CTACCGATTTTGTTATTTTTTTT
*
1454976 CTATCGATTTTGTTATT
1 CTACCGATTTTGTTATT
1454993 GTTAGGCACT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
22 14 0.38
23 23 0.62
ACGTcount: A:0.13, C:0.13, G:0.11, T:0.63
Consensus pattern (23 bp):
CTACCGATTTTGTTATTTTTTTT
Found at i:1455522 original size:20 final size:22
Alignment explanation
Indices: 1455489--1455531 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
1455479 TACTACTCTA
1455489 CATAGTAGTCGATACCA-TAGG
1 CATAGTAGTCGATACCATTAGG
1455510 CATAGTA-TCGATACCATTAGG
1 CATAGTAGTCGATACCATTAGG
1455531 C
1 C
1455532 CCCAACGGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (22 bp):
CATAGTAGTCGATACCATTAGG
Found at i:1460352 original size:12 final size:12
Alignment explanation
Indices: 1460335--1460359 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1460325 CGGAGACAAC
1460335 ATTTTATATTAA
1 ATTTTATATTAA
1460347 ATTTTATATTAA
1 ATTTTATATTAA
1460359 A
1 A
1460360 GGGTAAACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTTATATTAA
Found at i:1462265 original size:29 final size:29
Alignment explanation
Indices: 1462231--1462297 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
1462221 TAATTTATTC
1462231 ATATTATGT-ATGCCAACATTATTATTAAA
1 ATATTAT-TCATGCCAACATTATTATTAAA
** *
1462260 ATATTATTCATGTTAATATTATTATTAAA
1 ATATTATTCATGCCAACATTATTATTAAA
1462289 ATTATTATT
1 A-TATTATT
1462298 AGTATATTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 1 0.03
29 25 0.76
30 7 0.21
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.49
Consensus pattern (29 bp):
ATATTATTCATGCCAACATTATTATTAAA
Found at i:1462362 original size:22 final size:23
Alignment explanation
Indices: 1462337--1462379 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1462327 AATTATTAAT
1462337 TATTATTAAAA-AAAAATATATG
1 TATTATTAAAATAAAAATATATG
* *
1462359 TATTGTTAAAATAAGAATATA
1 TATTATTAAAATAAAAATATA
1462380 ATATTATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (23 bp):
TATTATTAAAATAAAAATATATG
Found at i:1462384 original size:22 final size:22
Alignment explanation
Indices: 1462337--1462386 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1462327 AATTATTAAT
*
1462337 TATTATTAAAAAAAAATATATG
1 TATTATTAAAAAAAAATATATA
* *
1462359 TATTGTTAAAATAAGAATATA-A
1 TATTATTAAAA-AAAAATATATA
1462381 TATTAT
1 TATTAT
1462387 ATATTATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (22 bp):
TATTATTAAAAAAAAATATATA
Found at i:1467113 original size:19 final size:19
Alignment explanation
Indices: 1467089--1467128 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1467079 AAAAAAAAAC
*
1467089 ATAATAT-AATATATATAAT
1 ATAATATCAATACATA-AAT
1467108 ATAATATCAATACATAAAT
1 ATAATATCAATACATAAAT
1467127 AT
1 AT
1467129 CTTTAAATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAATATCAATACATAAAT
Done.