Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 202 of 208
Found at i:61417853 original size:28 final size:29
Alignment explanation
Indices: 61417821--61417891 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 29
61417811 ATATTTTAGT
*
61417821 TAATATATATTATATTTATT-TACTTAATA
1 TAATATATATTATATTAATTATA-TTAATA
*
61417850 -AATA-AGTATTATATTAATTATATTATTA
1 TAATATA-TATTATATTAATTATATTAATA
61417878 TAATATTATATTAT
1 TAATA-TATATTAT
61417892 TATATATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
27 1 0.03
28 21 0.60
29 6 0.17
30 6 0.17
31 1 0.03
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (29 bp):
TAATATATATTATATTAATTATATTAATA
Found at i:61417879 original size:8 final size:8
Alignment explanation
Indices: 61417856--61417896 Score: 64
Period size: 8 Copynumber: 5.0 Consensus size: 8
61417846 AATAAATAAG
61417856 TATTATAT
1 TATTATAT
61417864 TAATTATAT
1 T-ATTATAT
*
61417873 TATTATAA
1 TATTATAT
61417881 TATTATAT
1 TATTATAT
61417889 TATTATAT
1 TATTATAT
61417897 ATATAAAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 22 0.73
9 8 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TATTATAT
Found at i:61418315 original size:15 final size:15
Alignment explanation
Indices: 61418295--61418324 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
61418285 TGAATATCGA
61418295 TATTGAATTAAATGT
1 TATTGAATTAAATGT
*
61418310 TATTGAATTATATGT
1 TATTGAATTAAATGT
61418325 GAATTGAATG
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:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (15 bp):
TATTGAATTAAATGT
Found at i:61421595 original size:3 final size:3
Alignment explanation
Indices: 61421587--61421633 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
61421577 TATAAACTAG
*
61421587 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
61421634 GAAACATATT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:61423327 original size:24 final size:26
Alignment explanation
Indices: 61423269--61423329 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 26
61423259 AACGTAATGA
61423269 TTCAAAT-ATTATAATAGAATAATTTT
1 TTCAAATCATTATAATAGAATAA-TTT
61423295 TTCTGAAATCATTATAATAGAAT-A-TT
1 TTC--AAATCATTATAATAGAATAATTT
61423321 TTCAAATCA
1 TTCAAATCA
61423330 AAATTAAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
24 6 0.19
26 8 0.25
28 5 0.16
29 13 0.41
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.43
Consensus pattern (26 bp):
TTCAAATCATTATAATAGAATAATTT
Found at i:61432264 original size:15 final size:15
Alignment explanation
Indices: 61432244--61432272 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
61432234 CTTAACATTG
61432244 TATTAAAAAGAACAT
1 TATTAAAAAGAACAT
61432259 TATTAAAAAGAACA
1 TATTAAAAAGAACA
61432273 GATATGATAA
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:0.62, C:0.07, G:0.07, T:0.24
Consensus pattern (15 bp):
TATTAAAAAGAACAT
Found at i:61446154 original size:17 final size:16
Alignment explanation
Indices: 61446130--61446166 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
61446120 TTTTACCCAT
61446130 TTTA-TTTTCATAATTA
1 TTTATTTTTCAT-ATTA
61446146 TTTATTTTTCATATTA
1 TTTATTTTTCATATTA
61446162 TTTAT
1 TTTAT
61446167 ATAAAAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTATTTTTCATATTA
Found at i:61448842 original size:3 final size:3
Alignment explanation
Indices: 61448828--61448901 Score: 51
Period size: 3 Copynumber: 24.3 Consensus size: 3
61448818 CAAACATTTA
* * * * *
61448828 TAT TAT TCAT TAT TAA TAT TAT TAA TGT TAT TGT TAT TAT CAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
61448874 TAT TGT TAT CAT T-T TCAT CAT TAT TAT T
1 TAT TAT TAT TAT TAT T-AT TAT TAT TAT T
61448902 GTTTATGCAT
Statistics
Matches: 52, Mismatches: 16, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
2 2 0.04
3 46 0.88
4 4 0.08
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:61458812 original size:14 final size:14
Alignment explanation
Indices: 61458793--61458821 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
61458783 GTCTTTGGTT
61458793 GGCTTACAGTTATC
1 GGCTTACAGTTATC
61458807 GGCTTACAGTTATC
1 GGCTTACAGTTATC
61458821 G
1 G
61458822 ACTTTGAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (14 bp):
GGCTTACAGTTATC
Found at i:61475664 original size:14 final size:15
Alignment explanation
Indices: 61475628--61475680 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
61475618 TAGAATTTCA
*
61475628 AAAGTTTAAAAATAT
1 AAAGATTAAAAATAT
*
61475643 AAAGATTAAAAATTT
1 AAAGATTAAAAATAT
*
61475658 CAA-ATT-AAAATAT
1 AAAGATTAAAAATAT
*
61475671 AAAGGTTAAA
1 AAAGATTAAA
61475681 TTCACAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
13 8 0.27
14 5 0.17
15 17 0.57
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (15 bp):
AAAGATTAAAAATAT
Found at i:61476963 original size:23 final size:21
Alignment explanation
Indices: 61476926--61476972 Score: 51
Period size: 23 Copynumber: 2.1 Consensus size: 21
61476916 AAATTAGCAC
61476926 AATTTTTTAAATTAAATT-AT
1 AATTTTTTAAATTAAATTAAT
*
61476946 AATTATTTTAAAACTTAATTTAAT
1 AATT-TTTT-AAA-TTAAATTAAT
61476970 AAT
1 AAT
61476973 ATGATAGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 4 0.18
21 4 0.18
22 3 0.14
23 6 0.27
24 5 0.23
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
AATTTTTTAAATTAAATTAAT
Found at i:61478724 original size:31 final size:30
Alignment explanation
Indices: 61478687--61478767 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 30
61478677 TACAAGCTAG
61478687 TGACTTAAATAGAAACTTTTAAATAGTTAAA
1 TGACTTAAAT-GAAACTTTTAAATAGTTAAA
* * *
61478718 TGACTTAAATGAAAATTTTTGAATAGTTTAA
1 TGACTTAAATG-AAACTTTTAAATAGTTAAA
*
61478749 TGAC-TAAATTGTAACTTTT
1 TGACTTAAA-TGAAACTTTT
61478768 TTAATTAAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
30 11 0.26
31 32 0.74
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.41
Consensus pattern (30 bp):
TGACTTAAATGAAACTTTTAAATAGTTAAA
Found at i:61481407 original size:20 final size:20
Alignment explanation
Indices: 61481362--61481410 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
61481352 TTTTCAACAA
*
61481362 AAAAAATTTAGAATAATTTT
1 AAAAAATTTAAAATAATTTT
*
61481382 TAAAAATTTAAAAT-ATTTAT
1 AAAAAATTTAAAATAATTT-T
61481402 AAAAAATTT
1 AAAAAATTT
61481411 CATAGTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
AAAAAATTTAAAATAATTTT
Found at i:61481596 original size:16 final size:16
Alignment explanation
Indices: 61481575--61481605 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
61481565 CTTTGAAAGA
61481575 ATTTCAAATATATATT
1 ATTTCAAATATATATT
*
61481591 ATTTCAAATTTATAT
1 ATTTCAAATATATAT
61481606 GCTCTAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTTCAAATATATATT
Found at i:61482098 original size:24 final size:23
Alignment explanation
Indices: 61482065--61482117 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 23
61482055 TTCTTAAAAA
* *
61482065 TAAAAGTAGATGGAATACATTCT
1 TAAAAGTAGAGGGAATAAATTCT
*
61482088 TAAAATGTAGAGGGACTAAATTCT
1 TAAAA-GTAGAGGGAATAAATTCT
61482112 TAAAAG
1 TAAAAG
61482118 AATAAAAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.45, C:0.08, G:0.19, T:0.28
Consensus pattern (23 bp):
TAAAAGTAGAGGGAATAAATTCT
Found at i:61482520 original size:15 final size:17
Alignment explanation
Indices: 61482480--61482518 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
61482470 ATAAAAATTA
61482480 TAAAAATTATATATTTT
1 TAAAAATTATATATTTT
*
61482497 TAATAAATT-TATTTTTT
1 TAA-AAATTATATATTTT
61482514 TAAAA
1 TAAAA
61482519 TTAATTCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 13 0.65
18 5 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TAAAAATTATATATTTT
Found at i:61483532 original size:25 final size:25
Alignment explanation
Indices: 61483475--61483532 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
61483465 ATTTTATATT
* *
61483475 TATATATTCTATACATAAATAATTA
1 TATATATTCAATACAAAAATAATTA
* *
61483500 TATTTATTCAATATAAAAATAAATTA
1 TATATATTCAATACAAAAAT-AATTA
61483526 -ATATATT
1 TATATATT
61483533 TATTTCTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 22 0.81
26 5 0.19
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (25 bp):
TATATATTCAATACAAAAATAATTA
Found at i:61486412 original size:36 final size:35
Alignment explanation
Indices: 61486335--61486417 Score: 148
Period size: 35 Copynumber: 2.3 Consensus size: 35
61486325 AAATATATCC
61486335 TTAATTTTAAATATTTTATTTTTTCTAAACAAAAA
1 TTAATTTTAAATATTTTATTTTTTCTAAACAAAAA
*
61486370 TTAATTTTAAATATTTTATTTTTTCTAAACAATAA
1 TTAATTTTAAATATTTTATTTTTTCTAAACAAAAA
61486405 TTAAATTTTAAAT
1 TT-AATTTTAAAT
61486418 GTAAAGTTTA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
35 36 0.78
36 10 0.22
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (35 bp):
TTAATTTTAAATATTTTATTTTTTCTAAACAAAAA
Found at i:61490265 original size:21 final size:20
Alignment explanation
Indices: 61490226--61490266 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
61490216 CATTTTTTTC
61490226 TTCTTTTTTACTGTCTTGTT
1 TTCTTTTTTACTGTCTTGTT
* *
61490246 TTCTTTATTTTCTTTCTTGTT
1 TTCTTT-TTTACTGTCTTGTT
61490267 CTTTAAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.05, C:0.15, G:0.07, T:0.73
Consensus pattern (20 bp):
TTCTTTTTTACTGTCTTGTT
Found at i:61493072 original size:7 final size:7
Alignment explanation
Indices: 61493060--61493098 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
61493050 TAGGGTGTAG
61493060 TAAAAAA
1 TAAAAAA
61493067 TAAAAAA
1 TAAAAAA
61493074 TAAAAAA
1 TAAAAAA
*
61493081 TATAAATA
1 TA-AAAAA
61493089 TAAATAAA
1 TAAA-AAA
61493097 TA
1 TA
61493099 TAATACTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
7 18 0.64
8 10 0.36
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
TAAAAAA
Found at i:61493079 original size:14 final size:15
Alignment explanation
Indices: 61493060--61493101 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
61493050 TAGGGTGTAG
61493060 TAAAAAATA-AAAAA
1 TAAAAAATATAAAAA
*
61493074 TAAAAAATATAAATA
1 TAAAAAATATAAAAA
61493089 TAAATAAATATAA
1 TAAA-AAATATAA
61493102 TACTTGTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 9 0.36
15 8 0.32
16 8 0.32
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
TAAAAAATATAAAAA
Found at i:61493085 original size:16 final size:16
Alignment explanation
Indices: 61493061--61493101 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
61493051 AGGGTGTAGT
61493061 AAAAA-ATAAAAAATA
1 AAAAATATAAAAAATA
*
61493076 AAAAATAT-AAATATA
1 AAAAATATAAAAAATA
61493091 AATAAATATAA
1 AA-AAATATAA
61493102 TACTTGTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 13 0.59
16 8 0.36
17 1 0.05
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAAATATAAAAAATA
Found at i:61493962 original size:16 final size:16
Alignment explanation
Indices: 61493940--61493983 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
61493930 CATATTATTT
*
61493940 TTAATTATTTTTATA-
1 TTAATTATTTTAATAG
61493955 TTATATTATTTTAATAG
1 TTA-ATTATTTTAATAG
61493972 TTAATTATTTTA
1 TTAATTATTTTA
61493984 TACAATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 3 0.12
16 20 0.77
17 3 0.12
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (16 bp):
TTAATTATTTTAATAG
Found at i:61502557 original size:2 final size:2
Alignment explanation
Indices: 61502550--61502580 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
61502540 ATTATTGTTT
61502550 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
61502581 TTGTATTTCT
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:61505163 original size:26 final size:26
Alignment explanation
Indices: 61505123--61505172 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
61505113 CGATTAATAA
*
61505123 TTTTTTGAAAGTTCGGTTCGGTTATT
1 TTTTTTGAAAGTTCGATTCGGTTATT
* * *
61505149 TTTTTTTAAATTTCGATTTGGTTA
1 TTTTTTGAAAGTTCGATTCGGTTA
61505173 ACAGTTTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.18, C:0.06, G:0.18, T:0.58
Consensus pattern (26 bp):
TTTTTTGAAAGTTCGATTCGGTTATT
Found at i:61509541 original size:16 final size:16
Alignment explanation
Indices: 61509520--61509551 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
61509510 TTCAATCATA
61509520 ATTAAAACATGAAGAT
1 ATTAAAACATGAAGAT
*
61509536 ATTAAAATATGAAGAT
1 ATTAAAACATGAAGAT
61509552 GAACCACTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.56, C:0.03, G:0.12, T:0.28
Consensus pattern (16 bp):
ATTAAAACATGAAGAT
Found at i:61513036 original size:25 final size:24
Alignment explanation
Indices: 61512998--61513047 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 24
61512988 GGTCCACGTG
*
61512998 TATTAATAATTATATATTTTTATAA
1 TATTAATAAATATATATTTTT-TAA
61513023 TATTAATAAATATATATTTTTTAA
1 TATTAATAAATATATATTTTTTAA
61513047 T
1 T
61513048 TTTTTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TATTAATAAATATATATTTTTTAA
Found at i:61518489 original size:27 final size:24
Alignment explanation
Indices: 61518429--61518491 Score: 63
Period size: 27 Copynumber: 2.4 Consensus size: 24
61518419 TATAAATAAT
61518429 TATATTAAAAGTTTGTAAAAATTA
1 TATATTAAAAGTTTGTAAAAATTA
*
61518453 TATCAGATTAAAATTTCATGTATAAAATTA
1 TAT---ATTAAAAGTT--TGTA-AAAATTA
61518483 TATATTAAA
1 TATATTAAA
61518492 TTAAAATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
24 3 0.09
27 15 0.47
29 4 0.12
30 10 0.31
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.41
Consensus pattern (24 bp):
TATATTAAAAGTTTGTAAAAATTA
Found at i:61518515 original size:19 final size:19
Alignment explanation
Indices: 61518473--61518517 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 19
61518463 AAATTTCATG
*
61518473 TATAAAATTATATATTAAA
1 TATAAAATTATATATAAAA
61518492 T-TAAAATT-TATATAAAA
1 TATAAAATTATATATAAAA
61518509 TTATAAAAT
1 -TATAAAAT
61518518 AATGAGAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 8 0.35
18 8 0.35
19 7 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TATAAAATTATATATAAAA
Found at i:61525304 original size:31 final size:31
Alignment explanation
Indices: 61525269--61525333 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
61525259 AATAGCTCAA
*
61525269 TGACTTAAATAAAAACTTTTGTATAGTTTAG
1 TGACTTAAATAAAAACTTTTGAATAGTTTAG
* *
61525300 TGACTTAAATGAAAACTTTTGAATGGTTTAG
1 TGACTTAAATAAAAACTTTTGAATAGTTTAG
61525331 TGA
1 TGA
61525334 TCAAATTGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.40
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTTGAATAGTTTAG
Found at i:61529870 original size:23 final size:23
Alignment explanation
Indices: 61529824--61529871 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
61529814 ATGAGTTTAT
* *
61529824 TTTTTTGTTTAAATTTAATTTAA
1 TTTTTTGTTTAAAATTAATCTAA
61529847 TTTTTT-TTTAAAATTAGATCTAA
1 TTTTTTGTTTAAAATTA-ATCTAA
61529870 TT
1 TT
61529872 CGATCCGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (23 bp):
TTTTTTGTTTAAAATTAATCTAA
Found at i:61543840 original size:6 final size:6
Alignment explanation
Indices: 61543829--61543863 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
61543819 TGGGCTTTTT
61543829 AAAATA AAAATA AAAATA AAAATA AAAATA AAAAT
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAAT
61543864 GGTGGGTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:61545279 original size:212 final size:214
Alignment explanation
Indices: 61544492--61545546 Score: 1460
Period size: 212 Copynumber: 4.9 Consensus size: 214
61544482 CTGTGAGCCT
* * ** * **
61544492 TGAGATAAAACCCGAAGCAGAATTAAGACACATCAGTATATATCCATTTGTATATCTCA-ATATA
1 TGAGATAAAACCCGAAGCAGAATTGAGACACATCAATATATATATATATCCATAT-T-ATATATA
** *
61544556 TATATAACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCGGCCACCTTATCTGTAAAAT
64 TATAT-ACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGTAAAAT
* * *
61544621 GTGATCATTTTGGCAAATATTCCATATTTAAGAACTTTCCTGGACAATTTTCTGAAACTATGACC
128 GTGATCATTTTAGCAAATATTCCAT-CTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGACC
*
61544686 CATCAAGGCTCTTGGCAGAATCG
192 CATCAAGGCTCTTAGCAGAATCG
* * **
61544709 TGAGATAAAACCTGAAGCAGAATTGAGACACATCAATATATATATCCATTTGTATATCTCAATAT
1 TGAGATAAAACCCGAAGCAGAATTGAGACACATCAATATATATAT--ATATCCATAT-T--ATAT
* *
61544774 ATATATATACATACGCATGTGTAGTTAGAATATTTGGACAAGTTGTCCTCTACCTTATCTGTAAA
61 ATATATATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGTAAA
*
61544839 ATGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAATTTTTCTG-AACTATGAC
126 ATGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGAC
*
61544903 CCATCAAGGCTCTTAGCAGAATGG
191 CCATCAAGGCTCTTAGCAGAATCG
* * * * **
61544927 TGAGATAAAACCCGAAGCAGAATTGCGACACTTCGATATGTATCCA-AT-TGTATATCTCA-ATA
1 TGAGATAAAACCCGAAGCAGAATTGAGACACATCAATATATAT--ATATATCCATAT-T-ATATA
* *
61544989 TATATATACATAGGCATGTCTAGTTAGACTATTTGGACAAGTTGTCATCTACCTTATCTGTAAAA
62 TATATATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGTAAAA
*
61545054 TGTGATTATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGACC
127 TGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGACC
* * *
61545119 CATCAAGACTGTTAGCAGAGTCG
192 CATCAAGGCTCTTAGCAGAATCG
* * *
61545142 TGAGATAGAACCCGAAGCAGAGTTGAGACACATCAATATATATATATATCCAT-TTGT-TATATA
1 TGAGATAAAACCCGAAGCAGAATTGAGACACATCAATATATATATATATCCATATTATATATATA
*
61545205 TATACATACGCATGTCTAGTTAGAATATTTGGTCAAGTTGTCATCTACCTTATCTGTAAAATGTG
66 TATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGTAAAATGTG
*
61545270 ATCATTTTAGCAAATATTCCATCTTAAGAACTTTGCTGGAAAATTTTCTGAAACTATGACCCATC
131 ATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGACCCATC
*
61545335 AAGGCTCTTAGCAGAGTCG
196 AAGGCTCTTAGCAGAATCG
* *
61545354 TGAGATAAAACCCAAAGCAGAATTGAGCCACATCAATATATATATATATCCATTTGTATATCTCA
1 TGAGATAAAACCCGAAGCAGAATTGAGACACATCAATATATATATATATCC------ATAT-T--
*
61545419 ATATATATATATACATACGCGTGTCTAGTTAGAAT-TTTGGACAAGTTGTCATCTACCTTATCTG
57 ATATATATATATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTG
*
61545483 TAAAATGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAATTTTTCTGAAACT
122 TAAAATGTGATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACT
61545547 TTTTTTTTCC
Statistics
Matches: 760, Mismatches: 57, Indels: 37
0.89 0.07 0.04
Matches are distributed among these distances:
212 195 0.26
213 2 0.00
214 119 0.16
215 70 0.09
216 9 0.01
217 42 0.06
218 71 0.09
219 38 0.05
220 82 0.11
221 10 0.01
222 91 0.12
223 31 0.04
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (214 bp):
TGAGATAAAACCCGAAGCAGAATTGAGACACATCAATATATATATATATCCATATTATATATATA
TATACATACGCATGTCTAGTTAGAATATTTGGACAAGTTGTCATCTACCTTATCTGTAAAATGTG
ATCATTTTAGCAAATATTCCATCTTAAGAACTTTCCTGGAAAATTTTCTGAAACTATGACCCATC
AAGGCTCTTAGCAGAATCG
Found at i:61546145 original size:59 final size:59
Alignment explanation
Indices: 61546066--61546187 Score: 208
Period size: 59 Copynumber: 2.1 Consensus size: 59
61546056 CTCACTTTTG
*
61546066 AATTAAAAGAGATTAAATTACTTCAAATTTTTTAGAGGATTCAATATGCTCAATTTCAA
1 AATTAAAAGAGATTAAATTACTTCAAATTTTTTAGAAGATTCAATATGCTCAATTTCAA
* * *
61546125 AATTAAAAGGGATTAAATTACTTTAATTTTTTTAGAAGATTCAATATGCTCAATTTCAA
1 AATTAAAAGAGATTAAATTACTTCAAATTTTTTAGAAGATTCAATATGCTCAATTTCAA
61546184 AATT
1 AATT
61546188 GAGAGAGACT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (59 bp):
AATTAAAAGAGATTAAATTACTTCAAATTTTTTAGAAGATTCAATATGCTCAATTTCAA
Found at i:61547992 original size:3 final size:3
Alignment explanation
Indices: 61547984--61548009 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
61547974 TGATTTCTTT
61547984 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
61548010 TTTAGTTCGG
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:61548440 original size:2 final size:2
Alignment explanation
Indices: 61548433--61548479 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
61548423 TGGATACAAC
61548433 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
61548475 AT AT A
1 AT AT A
61548480 CAATAAAATA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:61550673 original size:89 final size:91
Alignment explanation
Indices: 61550572--61550763 Score: 280
Period size: 93 Copynumber: 2.1 Consensus size: 91
61550562 TAAATAATAA
* * * *
61550572 AATTGCACATCCTATTTGATATTTTTGAGC-AAAAGAAA-AGAAAAGAATAATGACCTTGAATAC
1 AATTGCACATCCTATATGATATTTTTGAGCAAAAAAAAAGAGAAAAGAATAATAACCTTAAATAC
*
61550635 ATGGTATTAGAGCGACTTATGATTGC
66 ATGGTATTAGAGCGACCTATGATTGC
* *
61550661 AATTGCATATCCTATATGATATTTTTTAGCAAAAAAAAAAAGAGAAAAGAATAATAACCTTAAAT
1 AATTGCACATCCTATATGATATTTTTGAGC--AAAAAAAAAGAGAAAAGAATAATAACCTTAAAT
61550726 ACATGGTATTAGAGCGACCTATGATTGC
64 ACATGGTATTAGAGCGACCTATGATTGC
*
61550754 AATTCCACAT
1 AATTGCACAT
61550764 TGACTTCCCA
Statistics
Matches: 90, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
89 27 0.30
92 7 0.08
93 56 0.62
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (91 bp):
AATTGCACATCCTATATGATATTTTTGAGCAAAAAAAAAGAGAAAAGAATAATAACCTTAAATAC
ATGGTATTAGAGCGACCTATGATTGC
Found at i:61554715 original size:18 final size:17
Alignment explanation
Indices: 61554688--61554724 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
61554678 ATTTTTTATT
61554688 TTAAAAAATATTTAAAA
1 TTAAAAAATATTTAAAA
*
61554705 TTAATAAAATATTTATAA
1 TTAA-AAAATATTTAAAA
61554723 TT
1 TT
61554725 TTCAATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAAAAAATATTTAAAA
Found at i:61565165 original size:7 final size:7
Alignment explanation
Indices: 61565119--61565178 Score: 56
Period size: 7 Copynumber: 9.0 Consensus size: 7
61565109 CATTTTTTAA
*
61565119 TAAACAT
1 TAAAAAT
61565126 TAAAAA-
1 TAAAAAT
61565132 T-AAAA-
1 TAAAAAT
61565137 T-AAAAT
1 TAAAAAT
*
61565143 TAAAGTAT
1 TAAA-AAT
*
61565151 TTAAAAT
1 TAAAAAT
61565158 TAAAAAT
1 TAAAAAT
61565165 TAAAAAT
1 TAAAAAT
61565172 TAAAAAT
1 TAAAAAT
61565179 ATATATTTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
5 9 0.20
6 2 0.04
7 29 0.64
8 5 0.11
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (7 bp):
TAAAAAT
Found at i:61566284 original size:20 final size:20
Alignment explanation
Indices: 61566247--61566285 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
61566237 GAGGTTTAGG
*
61566247 GTTTAAGGTTTATAGTTTGA
1 GTTTAAGGTTTAGAGTTTGA
*
61566267 GTTTAAGGTTTAGGGTTTG
1 GTTTAAGGTTTAGAGTTTG
61566286 GGATTCATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.49
Consensus pattern (20 bp):
GTTTAAGGTTTAGAGTTTGA
Found at i:61568545 original size:30 final size:30
Alignment explanation
Indices: 61568510--61568642 Score: 160
Period size: 30 Copynumber: 4.4 Consensus size: 30
61568500 CCCCCAGTTT
* * *
61568510 CAACTCCTCCACCCAG-TTCTCCTCCTCCTG
1 CAACTCCACCA-CCAGCTTCTCCACCTCCCG
* * *
61568540 CAACTCCACCACCTGCTTCTCCTCCTCCTG
1 CAACTCCACCACCAGCTTCTCCACCTCCCG
*
61568570 CAACTCCACCTCCAGCTTCTCCACCTCCCG
1 CAACTCCACCACCAGCTTCTCCACCTCCCG
* *
61568600 CCACTCCTCCACCAGCTTCTCCACCTCCCG
1 CAACTCCACCACCAGCTTCTCCACCTCCCG
*
61568630 CCACTCCACCACC
1 CAACTCCACCACC
61568643 TGCAACCCCA
Statistics
Matches: 92, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
29 3 0.03
30 89 0.97
ACGTcount: A:0.15, C:0.57, G:0.06, T:0.22
Consensus pattern (30 bp):
CAACTCCACCACCAGCTTCTCCACCTCCCG
Found at i:61568546 original size:15 final size:15
Alignment explanation
Indices: 61568528--61568666 Score: 89
Period size: 15 Copynumber: 9.3 Consensus size: 15
61568518 CCACCCAGTT
*
61568528 CTCCTCCTCCTGCAA
1 CTCCACCTCCTGCAA
* **
61568543 CTCCACCACCTGCTT
1 CTCCACCTCCTGCAA
*
61568558 CTCCTCCTCCTGCAA
1 CTCCACCTCCTGCAA
* **
61568573 CTCCACCTCCAGCTT
1 CTCCACCTCCTGCAA
* *
61568588 CTCCACCTCCCGCCA
1 CTCCACCTCCTGCAA
* * * **
61568603 CTCCTCCACCAGCTT
1 CTCCACCTCCTGCAA
* *
61568618 CTCCACCTCCCGCCA
1 CTCCACCTCCTGCAA
*
61568633 CTCCACCACCTGCAA
1 CTCCACCTCCTGCAA
* * *
61568648 CCCCACCGCCAGCAA
1 CTCCACCTCCTGCAA
61568663 CTCC
1 CTCC
61568667 TCCTGCTGCT
Statistics
Matches: 92, Mismatches: 32, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
15 92 1.00
ACGTcount: A:0.16, C:0.58, G:0.07, T:0.19
Consensus pattern (15 bp):
CTCCACCTCCTGCAA
Found at i:61568582 original size:45 final size:45
Alignment explanation
Indices: 61568528--61568666 Score: 116
Period size: 45 Copynumber: 3.1 Consensus size: 45
61568518 CCACCCAGTT
* * ** * *
61568528 CTCCTCCTCCTGCAACTCCACCACCTGCTTCTCCTCCTCCTGCAA
1 CTCCACCTCCAGCAACTCCACCACCTGCCACTCCTCCACCAGCAA
** * * **
61568573 CTCCACCTCCAGCTTCTCCACCTCCCGCCACTCCTCCACCAGCTT
1 CTCCACCTCCAGCAACTCCACCACCTGCCACTCCTCCACCAGCAA
* * * * * *
61568618 CTCCACCTCCCGCCACTCCACCACCTGCAACCCCACCGCCAGCAA
1 CTCCACCTCCAGCAACTCCACCACCTGCCACTCCTCCACCAGCAA
61568663 CTCC
1 CTCC
61568667 TCCTGCTGCT
Statistics
Matches: 71, Mismatches: 23, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
45 71 1.00
ACGTcount: A:0.16, C:0.58, G:0.07, T:0.19
Consensus pattern (45 bp):
CTCCACCTCCAGCAACTCCACCACCTGCCACTCCTCCACCAGCAA
Found at i:61568666 original size:30 final size:30
Alignment explanation
Indices: 61568632--61568690 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
61568622 ACCTCCCGCC
*
61568632 ACTCCACCACCTGCAACCCCACCGCCAGCA
1 ACTCCACCACCTGCAACCCCACCACCAGCA
* ** *
61568662 ACTCCTCCTGCTGCTACCCCACCACCAGC
1 ACTCCACCACCTGCAACCCCACCACCAGC
61568691 TCCATTGGCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.22, C:0.56, G:0.10, T:0.12
Consensus pattern (30 bp):
ACTCCACCACCTGCAACCCCACCACCAGCA
Found at i:61576862 original size:20 final size:21
Alignment explanation
Indices: 61576837--61576875 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
61576827 TTTCAACTAC
*
61576837 AATTTAA-TTCCAAAACCAAA
1 AATTTAATTTACAAAACCAAA
61576857 AATTTAATTTACAAAACCA
1 AATTTAATTTACAAAACCA
61576876 TGAAAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.28
Consensus pattern (21 bp):
AATTTAATTTACAAAACCAAA
Found at i:61580556 original size:13 final size:13
Alignment explanation
Indices: 61580538--61580563 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
61580528 TTGTCCTAGT
61580538 GATTAAATTAAAA
1 GATTAAATTAAAA
61580551 GATTAAATTAAAA
1 GATTAAATTAAAA
61580564 ATAAGCTTTA
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:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (13 bp):
GATTAAATTAAAA
Found at i:61580781 original size:86 final size:85
Alignment explanation
Indices: 61580664--61580848 Score: 244
Period size: 86 Copynumber: 2.2 Consensus size: 85
61580654 CGCCACGACT
* * *
61580664 TTTAGCGGCGCTTTACTAGAAGCGCCGCTAAAGACCCTGATCTTTAGCGGCGCCTCGACAACAAA
1 TTTAGCGGCGCTTTACTACAAACGCCGCTAAAGACCATGATCTTTAGCGGCGCCTCGACAACAAA
*
61580729 CGCCACTAAAGAACCTAATC
66 CGCCACAAAAGAACCTAATC
* * *** *
61580749 TTTAGCGGCACTTTCACTACAAACGCCGCTAAAGACCATGATCTTTAGTGGCGCCTTTTCCACAA
1 TTTAGCGGCGCTTT-ACTACAAACGCCGCTAAAGACCATGATCTTTAGCGGCGCCTCGACAACAA
* * *
61580814 ATGCCGCAAAAGACCCTAATC
65 ACGCCACAAAAGAACCTAATC
61580835 TTTAGCGGCGCTTT
1 TTTAGCGGCGCTTT
61580849 GACCAAAAAT
Statistics
Matches: 85, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
85 13 0.15
86 72 0.85
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.24
Consensus pattern (85 bp):
TTTAGCGGCGCTTTACTACAAACGCCGCTAAAGACCATGATCTTTAGCGGCGCCTCGACAACAAA
CGCCACAAAAGAACCTAATC
Found at i:61580859 original size:43 final size:42
Alignment explanation
Indices: 61580664--61580868 Score: 178
Period size: 43 Copynumber: 4.8 Consensus size: 42
61580654 CGCCACGACT
* * * *
61580664 TTTAGCGGCGCTTTACTAGAAGCGCCGCTAAAGACCCTGATC
1 TTTAGCGGCGCTTTACCAAAAACGCCGCTAAAGACCCTAATC
** * *
61580706 TTTAGCGGCGCCTCGA-CAACAAACGCCACTAAAGAACCTAATC
1 TTTAGCGGCG-CTTTACCAA-AAACGCCGCTAAAGACCCTAATC
* * * * *
61580749 TTTAGCGGCACTTTCACTACAAACGCCGCTAAAGACCATGATC
1 TTTAGCGGCGCTTT-ACCAAAAACGCCGCTAAAGACCCTAATC
* * * * *
61580792 TTTAGTGGCGCCTTTTCCACAAATGCCGCAAAAGACCCTAATC
1 TTTAGCGGCG-CTTTACCAAAAACGCCGCTAAAGACCCTAATC
* *
61580835 TTTAGCGGCGCTTTGACCAAAAATGCCACTAAAG
1 TTTAGCGGCGCTTT-ACCAAAAACGCCGCTAAAG
61580869 GCCAAACACC
Statistics
Matches: 127, Mismatches: 30, Indels: 11
0.76 0.18 0.07
Matches are distributed among these distances:
42 17 0.13
43 105 0.83
44 5 0.04
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (42 bp):
TTTAGCGGCGCTTTACCAAAAACGCCGCTAAAGACCCTAATC
Found at i:61588766 original size:113 final size:113
Alignment explanation
Indices: 61588568--61589165 Score: 871
Period size: 113 Copynumber: 5.3 Consensus size: 113
61588558 AGATAAAATG
* *
61588568 TTTTTGCGGCGCTTTTTAAAAAACGCCGCTAAAGACTTGAGCATTAGCGGCGCTTATTCAGAAAC
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTT-TTCAGAAAC
61588633 GCCGCTAAAGACCCC-AAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
65 GCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* * *
61588681 TTTTTGCGGCACTTTTAAAAAAACGCTGCTAAACACCTGAGCATTAGCGGCGCTTTTCAGAAACG
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTTCAGAAACG
* * *
61588746 CTGCTAAAGACCCCAAAAACTCAGAAAACGGTGTCGTTTGGCTTAGGC
66 CCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* * * * ** *
61588794 TTTTTGCGGCGCTTTTAACAAAACGCCGCTAAAAGACTTGAGAATTAGCGGCGCATAACAGAAAT
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCT-AAAGACCTGAGCATTAGCGGCGCTTTTCAGAAAC
* *
61588859 GCCGCGAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGTTTAGGC
65 GCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* * * *
61588908 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCATTACAAAAATG
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTTCAGAAACG
* *
61588973 CCGCTAAAGACCCCAAAAACTCAGAAAACGGTACCGTTGGGTTTAGGC
66 CCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* *
61589021 TTTTTGCGGCGCTTTTAAAAAACCGCCGCTAAAGACCTG-GAATTAGCGGCGCTTTAT-AGAAAC
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTT-TCAGAAAC
*
61589084 GCCGCTAAAGACCCCCAAAAACTCAGAAAACGGTAG-CGTTTGGCTTAGGC
65 GCCGCTAAAGA-CCCCAAAAACTCAGAAAACGGT-GCCGTTGGGCTTAGGC
* *
61589134 TTTTTGCGGCGCTTTCAAATAAACGCCGCTAA
1 TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAA
61589166 TGCTTATTTT
Statistics
Matches: 438, Mismatches: 42, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
112 52 0.12
113 286 0.65
114 100 0.23
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (113 bp):
TTTTTGCGGCGCTTTTAAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCTTTTCAGAAACG
CCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
Found at i:61588981 original size:227 final size:225
Alignment explanation
Indices: 61588568--61589165 Score: 896
Period size: 227 Copynumber: 2.6 Consensus size: 225
61588558 AGATAAAATG
* *
61588568 TTTTTGCGGCGCTTTTTAAAAAACGCCGCTAAAGACTTGAGCATTAGCGGCGCTTATTCAGAAAC
1 TTTTTGCGGCGC-TTTTAAAAAACGCCGCTAAAGACTTGAGAATTAGCGGCGCTTA-ACAGAAAC
*
61588633 GCCGCTAAAGACCCC-AAAACTCAGAAAACGGTGCCGTTGGGCTTAGGCTTTTTGCGGCACTTTT
64 GCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGCTTTTTGCGGCGCTTTT
* * * * *
61588697 AAAAAAACGCTGCTAAACACCTGAGCATTAGCGGCGCTTTTCAGAAACGCTGCTAAAGACCCCAA
129 AAAAAAACGCCGCTAAACACCTGAGCATTAGCGGCGCATTACAAAAACGCCGCTAAAGACCCCAA
** *
61588762 AAACTCAGAAAACGGTGTCGTTTGGCTTAGGC
194 AAACTCAGAAAACGGTACCGTTGGGCTTAGGC
* *
61588794 TTTTTGCGGCGCTTTTAACAAAACGCCGCTAAAAGACTTGAGAATTAGCGGCGCATAACAGAAAT
1 TTTTTGCGGCGCTTTTAA-AAAACGCCGCT-AAAGACTTGAGAATTAGCGGCGCTTAACAGAAAC
* *
61588859 GCCGCGAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGTTTAGGCTTTTTGCGGCGCTTTT
64 GCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGCTTTTTGCGGCGCTTTT
* *
61588924 AAAAAAACGCCGCTAAAGACCTGAGCATTAGCGGCGCATTACAAAAATGCCGCTAAAGACCCCAA
129 AAAAAAACGCCGCTAAACACCTGAGCATTAGCGGCGCATTACAAAAACGCCGCTAAAGACCCCAA
*
61588989 AAACTCAGAAAACGGTACCGTTGGGTTTAGGC
194 AAACTCAGAAAACGGTACCGTTGGGCTTAGGC
* * *
61589021 TTTTTGCGGCGCTTTTAAAAAACCGCCGCTAAAGACCTG-GAATTAGCGGCGCTTTATAGAAACG
1 TTTTTGCGGCGCTTTTAAAAAA-CGCCGCTAAAGACTTGAGAATTAGCGGCGCTTAACAGAAACG
*
61589085 CCGCTAAAGACCCCCAAAAACTCAGAAAACGGTAG-CGTTTGGCTTAGGCTTTTTGCGGCGCTTT
65 CCGCTAAAGA-CCCCAAAAACTCAGAAAACGGT-GCCGTTGGGCTTAGGCTTTTTGCGGCGCTTT
* *
61589149 CAAATAAACGCCGCTAA
128 TAAAAAAACGCCGCTAA
61589166 TGCTTATTTT
Statistics
Matches: 338, Mismatches: 28, Indels: 12
0.89 0.07 0.03
Matches are distributed among these distances:
225 36 0.11
226 119 0.35
227 183 0.54
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (225 bp):
TTTTTGCGGCGCTTTTAAAAAACGCCGCTAAAGACTTGAGAATTAGCGGCGCTTAACAGAAACGC
CGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGCTTTTTGCGGCGCTTTTAA
AAAAACGCCGCTAAACACCTGAGCATTAGCGGCGCATTACAAAAACGCCGCTAAAGACCCCAAAA
ACTCAGAAAACGGTACCGTTGGGCTTAGGC
Found at i:61589258 original size:40 final size:39
Alignment explanation
Indices: 61589134--61589268 Score: 132
Period size: 40 Copynumber: 3.4 Consensus size: 39
61589124 TGGCTTAGGC
* *
61589134 TTTTT-GCGGCGCTTTCAAATAAACGCCGCTAATGCTT-A
1 TTTTTAGCGGCGTTTTTAAA-AAACGCCGCTAATGCTTGA
** *
61589172 TTTTTAGCGGCGATTTTTAAAAAACGCCGCTAATAATCGA
1 TTTTTAGCGGCG-TTTTTAAAAAACGCCGCTAATGCTTGA
** *
61589212 CCTTTAGCGGCGTTTTCCT-AAAAGCGCCGCTAATGCTTGA
1 TTTTTAGCGGCGTTTT--TAAAAAACGCCGCTAATGCTTGA
*
61589252 TTTTTAGTGGCGTTTTT
1 TTTTTAGCGGCGTTTTT
61589269 TGTCTAATCG
Statistics
Matches: 78, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
38 6 0.08
39 24 0.31
40 47 0.60
41 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (39 bp):
TTTTTAGCGGCGTTTTTAAAAAACGCCGCTAATGCTTGA
Found at i:61590227 original size:9 final size:9
Alignment explanation
Indices: 61590213--61590237 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
61590203 TTTCTTATTT
61590213 TCAAGAAAA
1 TCAAGAAAA
61590222 TCAAGAAAA
1 TCAAGAAAA
61590231 TCAAGAA
1 TCAAGAA
61590238 GCCAATGCGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.64, C:0.12, G:0.12, T:0.12
Consensus pattern (9 bp):
TCAAGAAAA
Found at i:61592289 original size:8 final size:8
Alignment explanation
Indices: 61592276--61592300 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
61592266 AATCAAATAT
61592276 TATAATTA
1 TATAATTA
61592284 TATAATTA
1 TATAATTA
61592292 TATAATTA
1 TATAATTA
61592300 T
1 T
61592301 CCTTGTAATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TATAATTA
Found at i:61592601 original size:31 final size:30
Alignment explanation
Indices: 61592562--61592636 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
61592552 TTAATAATTT
*
61592562 AAGA-TAAAATTTGAAATATGAAAAATAAAA
1 AAGATTAAAATTTGAAAAAT-AAAAATAAAA
* *
61592592 AAGATTAAAATTTTAAAAATAAAAATACAA
1 AAGATTAAAATTTGAAAAATAAAAATAAAA
61592622 AA-ATTATAAATTTGA
1 AAGATTA-AAATTTGA
61592637 CTAAAATCTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 4 0.10
30 22 0.56
31 13 0.33
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.28
Consensus pattern (30 bp):
AAGATTAAAATTTGAAAAATAAAAATAAAA
Found at i:61604005 original size:30 final size:31
Alignment explanation
Indices: 61603952--61604037 Score: 97
Period size: 30 Copynumber: 2.8 Consensus size: 31
61603942 AGAAAAAGCA
* *
61603952 GTTTAATT-AAAGTTTTAAAAAATTTTGAGG
1 GTTTAATTGAAACTTTTAAAAAATTTAGAGG
* *
61603982 GTTTGA-TGAGAA-TTTTTAAAAATTTAGAGG
1 GTTTAATTGA-AACTTTTAAAAAATTTAGAGG
*
61604012 GTTTAATTGAAACTTTTCAAAAATTT
1 GTTTAATTGAAACTTTTAAAAAATTT
61604038 GAAAGGTATA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
29 1 0.02
30 29 0.62
31 17 0.36
ACGTcount: A:0.38, C:0.02, G:0.16, T:0.43
Consensus pattern (31 bp):
GTTTAATTGAAACTTTTAAAAAATTTAGAGG
Found at i:61607554 original size:12 final size:12
Alignment explanation
Indices: 61607534--61607568 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
61607524 GGGGGAGGAG
*
61607534 ACACACACACAC
1 ACACGCACACAC
*
61607546 ACACGCACACGC
1 ACACGCACACAC
61607558 ACACGCACACA
1 ACACGCACACA
61607569 GATCTTCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.43, C:0.49, G:0.09, T:0.00
Consensus pattern (12 bp):
ACACGCACACAC
Found at i:61609892 original size:16 final size:15
Alignment explanation
Indices: 61609851--61609904 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 15
61609841 AATAAAATTT
61609851 TATTTTTA-TTTA-A
1 TATTTTTATTTTATA
61609864 TATTTATTAATTTTATA
1 TATTT-TT-ATTTTATA
61609881 TACTTTTTATTTTATA
1 TA-TTTTTATTTTATA
*
61609897 AATTTTTA
1 TATTTTTA
61609905 AACCTAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
13 5 0.14
14 2 0.06
15 7 0.20
16 13 0.37
17 5 0.14
18 3 0.09
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTTTATTTTATA
Found at i:61614977 original size:12 final size:12
Alignment explanation
Indices: 61614962--61614987 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
61614952 AAATGCTTCT
61614962 TAAAAGCAATAC
1 TAAAAGCAATAC
61614974 TAAAAGCAATAC
1 TAAAAGCAATAC
61614986 TA
1 TA
61614988 TGTGTACTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.15, G:0.08, T:0.19
Consensus pattern (12 bp):
TAAAAGCAATAC
Found at i:61618462 original size:3 final size:3
Alignment explanation
Indices: 61618456--61618484 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
61618446 TAATAATAAT
61618456 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
61618485 TAAAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:61619390 original size:9 final size:9
Alignment explanation
Indices: 61619316--61619505 Score: 103
Period size: 9 Copynumber: 21.0 Consensus size: 9
61619306 TTTTAATACA
61619316 ATAA-TTTT
1 ATAATTTTT
*
61619324 ATATTTTTT
1 ATAATTTTT
* *
61619333 ACAAATTTT
1 ATAATTTTT
61619342 AT-ATTTATT
1 ATAATTT-TT
61619351 -TACATTTTT
1 ATA-ATTTTT
61619360 ATAATTTTCT
1 ATAATTTT-T
**
61619370 -TACAACTTT
1 ATA-ATTTTT
61619379 ATAATTTTT
1 ATAATTTTT
61619388 ATAATTTTCCT
1 ATAATTTT--T
*
61619399 AT-ATTTCT
1 ATAATTTTT
61619407 AT-ATATTTT
1 ATAAT-TTTT
61619416 ATAATTTTT
1 ATAATTTTT
*
61619425 CTAATTTTT
1 ATAATTTTT
61619434 A-AATTTTT
1 ATAATTTTT
*
61619442 CTAATTTTTT
1 ATAA-TTTTT
*
61619452 ATTAAAATTTTA
1 A-T--AATTTTT
61619464 ATAA-TTTT
1 ATAATTTTT
*
61619472 ATAACTTTT
1 ATAATTTTT
*
61619481 ATTATTTTT
1 ATAATTTTT
61619490 AT--TTTTT
1 ATAATTTTT
*
61619497 ATCATTTTT
1 ATAATTTTT
61619506 TGTCACATGG
Statistics
Matches: 142, Mismatches: 20, Indels: 39
0.71 0.10 0.19
Matches are distributed among these distances:
7 7 0.05
8 26 0.18
9 74 0.52
10 23 0.16
11 5 0.04
12 5 0.04
13 2 0.01
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (9 bp):
ATAATTTTT
Found at i:61619395 original size:37 final size:36
Alignment explanation
Indices: 61619316--61619440 Score: 100
Period size: 37 Copynumber: 3.4 Consensus size: 36
61619306 TTTTAATACA
61619316 ATAA-TTTTATATTTT-TTACAAATTT-TATATTTATT
1 ATAATTTTTATATTTTCTTACAAATTTATA-ATTT-TT
*
61619351 -TACATTTTTATAATTTTCTTACAACTTTATAATTTTT
1 ATA-ATTTTTAT-ATTTTCTTACAAATTTATAATTTTT
* *
61619388 ATAATTTTCCTATA-TTTCTATA-TATTTTATAATTTTT
1 ATAATTTT--TATATTTTCT-TACAAATTTATAATTTTT
* *
61619425 CTAATTTTTAAATTTT
1 ATAATTTTTATATTTT
61619441 TCTAATTTTT
Statistics
Matches: 75, Mismatches: 5, Indels: 19
0.76 0.05 0.19
Matches are distributed among these distances:
34 2 0.03
35 4 0.05
36 9 0.12
37 37 0.49
38 18 0.24
39 5 0.07
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (36 bp):
ATAATTTTTATATTTTCTTACAAATTTATAATTTTT
Found at i:61619409 original size:28 final size:26
Alignment explanation
Indices: 61619354--61619449 Score: 88
Period size: 28 Copynumber: 3.5 Consensus size: 26
61619344 ATTTATTTAC
* *
61619354 ATTTTTATAATTTTCTTACAACTTTATA
1 ATTTTTATAATTTTCCT--AATTTTATA
61619382 ATTTTTATAATTTTCCTATATTTCTAT-
1 ATTTTTATAATTTTCCTA-ATTT-TATA
*
61619409 ATATTTTATAATTTTTCTAATTTT-TAA
1 AT-TTTTATAATTTTCCTAATTTTAT-A
*
61619436 ATTTTTCTAATTTT
1 ATTTTTATAATTTT
61619450 TTATTAAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
25 1 0.02
26 13 0.22
27 11 0.19
28 34 0.58
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.62
Consensus pattern (26 bp):
ATTTTTATAATTTTCCTAATTTTATA
Found at i:61619443 original size:37 final size:36
Alignment explanation
Indices: 61619376--61619471 Score: 93
Period size: 37 Copynumber: 2.6 Consensus size: 36
61619366 TTCTTACAAC
**
61619376 TTTATAATTTTTATAATTTTCCTATATTTCTATATAT
1 TTTATAATTTTTATAATTTTCAAATATTTCTA-ATAT
* * * *
61619413 TTTATAATTTTTCTAATTTTTAAATTTTTCTAATTT
1 TTTATAATTTTTATAATTTTCAAATATTTCTAATAT
*
61619449 TTTATTAAAATTTTAATAATTTT
1 TTTA-T--AATTTTTATAATTTT
61619472 ATAACTTTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
36 7 0.15
37 28 0.58
39 13 0.27
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (36 bp):
TTTATAATTTTTATAATTTTCAAATATTTCTAATAT
Found at i:61619450 original size:17 final size:18
Alignment explanation
Indices: 61619320--61619450 Score: 85
Period size: 17 Copynumber: 7.2 Consensus size: 18
61619310 AATACAATAA
* *
61619320 TTTTATATTTTTTAC-AAA
1 TTTTATAATTTTT-CTAAT
61619338 TTTTAT-ATTTATT-TACAT
1 TTTTATAATTT-TTCTA-AT
*
61619356 TTTTATAA-TTTTCTTACAA
1 TTTTATAATTTTTC-TA-AT
* *
61619375 CTTTATAATTTTTATAAT
1 TTTTATAATTTTTCTAAT
** *
61619393 TTTCCT-ATATTTCTATAT
1 TTTTATAATTTTTCTA-AT
61619411 ATTTTATAATTTTTCTAAT
1 -TTTTATAATTTTTCTAAT
61619430 TTTTA-AATTTTTCTAAT
1 TTTTATAATTTTTCTAAT
61619447 TTTT
1 TTTT
61619451 TATTAAAATT
Statistics
Matches: 89, Mismatches: 14, Indels: 21
0.72 0.11 0.17
Matches are distributed among these distances:
17 29 0.33
18 28 0.31
19 20 0.22
20 12 0.13
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTATAATTTTTCTAAT
Found at i:61632992 original size:21 final size:21
Alignment explanation
Indices: 61632968--61633007 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
61632958 ATAGAGGTGT
*
61632968 TACATTAAAAT-TTATATTTAA
1 TACAATAAAATATT-TATTTAA
61632989 TACAATAAAATATTTATTT
1 TACAATAAAATATTTATTT
61633008 GTATTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (21 bp):
TACAATAAAATATTTATTTAA
Found at i:61633463 original size:16 final size:16
Alignment explanation
Indices: 61633442--61633475 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
61633432 GAGTAAACGT
61633442 GGAAGAAAG-GAAGAAG
1 GGAAGAAAGTG-AGAAG
61633458 GGAAGAAAGTGAGAAG
1 GGAAGAAAGTGAGAAG
61633474 GG
1 GG
61633476 GCAAAGGTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 16 0.94
17 1 0.06
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (16 bp):
GGAAGAAAGTGAGAAG
Found at i:61643150 original size:6 final size:6
Alignment explanation
Indices: 61643139--61643170 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
61643129 CAAAAGTTTT
61643139 ATATAG ATATAG ATATAG ATATAG ATATAG AT
1 ATATAG ATATAG ATATAG ATATAG ATATAG AT
61643171 GCAAATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (6 bp):
ATATAG
Found at i:61644094 original size:21 final size:19
Alignment explanation
Indices: 61644051--61644098 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
61644041 TATTTAAAGG
* *
61644051 ATTTAAAATAAATATAAAT
1 ATTTAAAATAAAAATAAAA
61644070 ATTTAAAACTAAACAATAAAA
1 ATTTAAAA-TAAA-AATAAAA
61644091 ATTTAAAA
1 ATTTAAAA
61644099 GTTGAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 8 0.32
20 4 0.16
21 13 0.52
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (19 bp):
ATTTAAAATAAAAATAAAA
Found at i:61645976 original size:16 final size:17
Alignment explanation
Indices: 61645942--61645979 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
61645932 TAATTGTTTA
*
61645942 AAATTTTTAAAAAATAT
1 AAATTATTAAAAAATAT
*
61645959 AAATTATTAAAATA-AT
1 AAATTATTAAAAAATAT
61645975 AAATT
1 AAATT
61645980 TACATTTAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATTATTAAAAAATAT
Found at i:61656157 original size:16 final size:16
Alignment explanation
Indices: 61656136--61656178 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
61656126 CTTTAGTTTT
61656136 TTTTTAAAATTTATAA
1 TTTTTAAAATTTATAA
*
61656152 TTTTTAAAA-ATATAA
1 TTTTTAAAATTTATAA
* *
61656167 ATTTTAGAATTT
1 TTTTTAAAATTT
61656179 TTATAAATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
TTTTTAAAATTTATAA
Found at i:61656172 original size:24 final size:24
Alignment explanation
Indices: 61656140--61656188 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
61656130 AGTTTTTTTT
*
61656140 TAAAATTTATAATTTTTAAAAATA
1 TAAAATTTAGAATTTTTAAAAATA
* *
61656164 TAAATTTTAGAATTTTTATAAATA
1 TAAAATTTAGAATTTTTAAAAATA
61656188 T
1 T
61656189 TTAGAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
TAAAATTTAGAATTTTTAAAAATA
Found at i:61656185 original size:18 final size:19
Alignment explanation
Indices: 61656162--61656198 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
61656152 TTTTTAAAAA
61656162 TATAAAT-TTTAGAATTTT
1 TATAAATATTTAGAATTTT
61656180 TATAAATATTTAGAATTTT
1 TATAAATATTTAGAATTTT
61656199 AAAAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:61656208 original size:19 final size:19
Alignment explanation
Indices: 61656165--61656224 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 19
61656155 TTAAAAATAT
*
61656165 AAAT-TTTAGAATTTTTAT
1 AAATATTTAGAATTTTTAA
61656183 AAATATTTAGAA-TTTTAA
1 AAATATTTAGAATTTTTAA
*
61656201 AAATTATTTTA-AATTTTTTA
1 AAA-TA-TTTAGAATTTTTAA
61656221 AAAT
1 AAAT
61656225 TGTTTTAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
18 12 0.33
19 12 0.33
20 12 0.33
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (19 bp):
AAATATTTAGAATTTTTAA
Found at i:61656239 original size:20 final size:20
Alignment explanation
Indices: 61656167--61656238 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 20
61656157 AAAAATATAA
61656167 ATTTTAGAA-TTTTTATAAA-T
1 ATTTTA-AATTTTTTA-AAATT
*
61656187 A-TTTAGAA-TTTTAAAAATT
1 ATTTTA-AATTTTTTAAAATT
61656206 ATTTTAAATTTTTTAAAATT
1 ATTTTAAATTTTTTAAAATT
*
61656226 GTTTT-AATTTTTT
1 ATTTTAAATTTTTT
61656239 TGCTATTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
18 3 0.07
19 24 0.52
20 19 0.41
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (20 bp):
ATTTTAAATTTTTTAAAATT
Found at i:61660389 original size:21 final size:21
Alignment explanation
Indices: 61660346--61660390 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
61660336 AATATAAAAG
*
61660346 AAAAATCAAAATTTAAATCTT
1 AAAAATCAAAATTTAAAGCTT
* *
61660367 AAAAATCAAAGTTTAAAGGTT
1 AAAAATCAAAATTTAAAGCTT
61660388 AAA
1 AAA
61660391 TTTTAGTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.29
Consensus pattern (21 bp):
AAAAATCAAAATTTAAAGCTT
Found at i:61667712 original size:2 final size:2
Alignment explanation
Indices: 61667659--61667693 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
61667649 CACCTTTTAT
61667659 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
61667694 TTGTGTGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:61668477 original size:2 final size:2
Alignment explanation
Indices: 61668470--61668514 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
61668460 TGTGGATGAT
61668470 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
61668512 TA T
1 TA T
61668515 TTAATTAATA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:61670397 original size:20 final size:19
Alignment explanation
Indices: 61670350--61670396 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
61670340 GTTTCTTTTA
61670350 TAAATTTTGTTAATAATTT
1 TAAATTTTGTTAATAATTT
* *
61670369 TATGATTTTTTTAATAATTT
1 TA-AATTTTGTTAATAATTT
61670389 TAAATTTT
1 TAAATTTT
61670397 TAAAAGGGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (19 bp):
TAAATTTTGTTAATAATTT
Found at i:61677405 original size:9 final size:9
Alignment explanation
Indices: 61677391--61677502 Score: 54
Period size: 9 Copynumber: 12.2 Consensus size: 9
61677381 TTTCAAGATA
61677391 TAATATTTT
1 TAATATTTT
61677400 TAATATTTTT
1 TAATA-TTTT
* *
61677410 TAAAATTTA
1 TAATATTTT
61677419 T-ATATTTT
1 TAATATTTT
*
61677427 T-GTAATTTT
1 TAAT-ATTTT
*
61677436 T-ACATTTT
1 TAATATTTT
61677444 TACAT-TTTCT
1 TA-ATATTT-T
*
61677454 TAATTTTTT
1 TAATATTTT
*
61677463 TATAAATTTT
1 TA-ATATTTT
61677473 ATAATAATTTT
1 -TAAT-ATTTT
* *
61677484 CAA-ATTTC
1 TAATATTTT
61677492 TAATATTTT
1 TAATATTTT
61677501 TA
1 TA
61677503 TAATTTCTTA
Statistics
Matches: 78, Mismatches: 15, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
8 19 0.24
9 29 0.37
10 23 0.29
11 7 0.09
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (9 bp):
TAATATTTT
Found at i:61677442 original size:25 final size:25
Alignment explanation
Indices: 61677414--61677461 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
61677404 ATTTTTTAAA
*
61677414 ATTTATATATTTT-TGTAATTTTTAC
1 ATTTATACATTTTCT-TAATTTTTAC
*
61677439 ATTTTTACATTTTCTTAATTTTT
1 ATTTATACATTTTCTTAATTTTT
61677462 TTATAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 19 0.95
26 1 0.05
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (25 bp):
ATTTATACATTTTCTTAATTTTTAC
Found at i:61677501 original size:18 final size:18
Alignment explanation
Indices: 61677460--61677510 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 18
61677450 TTCTTAATTT
*
61677460 TTTTATAAATTTTATAATAA
1 TTTTAT-AA-TTTCTAATAA
*
61677480 TTTTCA-AATTTCTAATAT
1 TTTT-ATAATTTCTAATAA
61677498 TTTTATAATTTCT
1 TTTTATAATTTCT
61677511 TATAGTTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 1 0.04
18 19 0.70
19 2 0.07
20 4 0.15
21 1 0.04
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTATAATTTCTAATAA
Found at i:61680554 original size:31 final size:32
Alignment explanation
Indices: 61680516--61680590 Score: 100
Period size: 31 Copynumber: 2.4 Consensus size: 32
61680506 TCAACGGCTC
*
61680516 AGTGACTAAAATGTTACAACATATT-AA-CATA
1 AGTGACTAAAATGTAACAACAT-TTCAAGCATA
*
61680547 AGTGACTAAAATGTAACAATATTTCAAGCATA
1 AGTGACTAAAATGTAACAACATTTCAAGCATA
*
61680579 GGTGACTAAAAT
1 AGTGACTAAAAT
61680591 ATAATATGAG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
30 2 0.05
31 22 0.56
32 15 0.38
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.28
Consensus pattern (32 bp):
AGTGACTAAAATGTAACAACATTTCAAGCATA
Found at i:61681442 original size:25 final size:23
Alignment explanation
Indices: 61681395--61681447 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 23
61681385 CTTCTCCAAT
61681395 TTAACTTTAATTAATTAAAAAAAA
1 TTAACTTTAATTAA-TAAAAAAAA
61681419 CTTAACTTTAATTAA-AAATTAAAAA
1 -TTAACTTTAATTAATAAA--AAAAA
61681444 TTAA
1 TTAA
61681448 AAAATAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.12
24 4 0.15
25 19 0.73
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (23 bp):
TTAACTTTAATTAATAAAAAAAA
Found at i:61686279 original size:21 final size:21
Alignment explanation
Indices: 61686238--61686308 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
61686228 ACGTTATAAA
**
61686238 ATATAAAAAATGGA-AATAAAT
1 ATATAAAAAATCTAGAA-AAAT
*
61686259 ATATAAAAAATTTAGAAAAAT
1 ATATAAAAAATCTAGAAAAAT
* * *
61686280 GTATAAATAATCTAGAAAAAAA
1 ATATAAAAAATCTAG-AAAAAT
61686302 ATATAAA
1 ATATAAA
61686309 TTATAAAAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
21 28 0.68
22 13 0.32
ACGTcount: A:0.66, C:0.01, G:0.07, T:0.25
Consensus pattern (21 bp):
ATATAAAAAATCTAGAAAAAT
Found at i:61686516 original size:18 final size:20
Alignment explanation
Indices: 61686495--61686541 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
61686485 TAAATACATG
61686495 TTTTAATTTTTATA-AT-AT
1 TTTTAATTTTTATATATGAT
61686513 TTTTCAA-TTTTATATATGAT
1 TTTT-AATTTTTATATATGAT
*
61686533 TTTGAATTT
1 TTTTAATTT
61686542 CTAAAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 11 0.46
19 6 0.25
20 7 0.29
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (20 bp):
TTTTAATTTTTATATATGAT
Found at i:61687353 original size:109 final size:110
Alignment explanation
Indices: 61687124--61687413 Score: 442
Period size: 109 Copynumber: 2.6 Consensus size: 110
61687114 GTTAAACGTG
* *
61687124 AAATCGAAACCCAGCACCTTAGGGCACGTTTCTCGAATTCCCAAACGCAAAACATTGCCTTATTT
1 AAATCGACACCCAGCACCTTAGGGCACGTTTCTCGAATTTCCAAACGCAAAACATTGCCTTA-TT
* * *
61687189 TTGAAAAGTTTTTTTAAAGGATATTTAGCTATTTGGTTGAATGAGAA
65 TTGAAAAG-TTTTTAAAAGGATATTGAGCTATTTGGTTGAACGAGAA
61687236 AAATCGACACCCAGCACCTTAGGGCACGCTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
1 AAATCGACACCCAGCACCTTAGGGCACG-TTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
*
61687301 TT-AAAA-TTTTTAAAAGGATATTGAG-TCATTTGGTTTAACGAGAA
65 TTGAAAAGTTTTTAAAAGGATATTGAGCT-ATTTGGTTGAACGAGAA
*
61687345 AAATCGACACCCAGCACCTTAGGGCACGTTTTTCTCGAATCTCCAAACGCAAAACATTGCCTTAT
1 AAATCGACACCCAGCACCTTAGGGCACG--TTTCTCGAATTTCCAAACGCAAAACATTGCCTTAT
61687410 TTTG
64 TTTG
61687414 GAACAATTTC
Statistics
Matches: 166, Mismatches: 8, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
108 1 0.01
109 60 0.36
110 37 0.22
111 4 0.02
112 31 0.19
113 33 0.20
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.30
Consensus pattern (110 bp):
AAATCGACACCCAGCACCTTAGGGCACGTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTT
TGAAAAGTTTTTAAAAGGATATTGAGCTATTTGGTTGAACGAGAA
Found at i:61687768 original size:2 final size:2
Alignment explanation
Indices: 61687761--61687786 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
61687751 GTATGTGGAC
61687761 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
61687787 TACAAAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61689155 original size:15 final size:15
Alignment explanation
Indices: 61689135--61689165 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
61689125 AATTTTTAGA
61689135 ATTTTAGAATTATAT
1 ATTTTAGAATTATAT
*
61689150 ATTTTAGAATTTTAT
1 ATTTTAGAATTATAT
61689165 A
1 A
61689166 AAAAATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (15 bp):
ATTTTAGAATTATAT
Found at i:61689256 original size:15 final size:15
Alignment explanation
Indices: 61689236--61689268 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
61689226 ATATTATTAA
61689236 TTTCAATTAAT-TTAT
1 TTTCAATT-ATCTTAT
61689251 TTTCAATTATCTTAT
1 TTTCAATTATCTTAT
61689266 TTT
1 TTT
61689269 TTATATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 2 0.12
15 15 0.88
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTCAATTATCTTAT
Found at i:61689286 original size:18 final size:18
Alignment explanation
Indices: 61689265--61689306 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
61689255 AATTATCTTA
*
61689265 TTTTTTAT-ATTTATAAT
1 TTTTTTATAATTTATAGT
61689282 TTTTTTATAATTTATATGT
1 TTTTTTATAATTTATA-GT
61689301 TTTTTT
1 TTTTTT
61689307 TTCTAGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.36
18 7 0.32
19 7 0.32
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (18 bp):
TTTTTTATAATTTATAGT
Found at i:61689307 original size:21 final size:23
Alignment explanation
Indices: 61689281--61689327 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
61689271 ATATTTATAA
*
61689281 TTTTTTTATA-A-TTTATATGTT
1 TTTTTTTATAGATTTTATATATT
*
61689302 TTTTTTTCTAGATTTTATATATT
1 TTTTTTTATAGATTTTATATATT
61689325 TTT
1 TTT
61689328 ATGAAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 1 0.05
23 12 0.55
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.72
Consensus pattern (23 bp):
TTTTTTTATAGATTTTATATATT
Found at i:61691828 original size:27 final size:28
Alignment explanation
Indices: 61691790--61691845 Score: 96
Period size: 27 Copynumber: 2.0 Consensus size: 28
61691780 AAAAAATTAT
61691790 TTTAAAAATATTTTAAAA-TTAAAAAAA
1 TTTAAAAATATTTTAAAATTTAAAAAAA
*
61691817 TTTAAAAGTATTTTAAAATTTAAAAAAA
1 TTTAAAAATATTTTAAAATTTAAAAAAA
61691845 T
1 T
61691846 AAAAAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (28 bp):
TTTAAAAATATTTTAAAATTTAAAAAAA
Found at i:61695108 original size:29 final size:30
Alignment explanation
Indices: 61695070--61695179 Score: 98
Period size: 29 Copynumber: 3.7 Consensus size: 30
61695060 ATATTTTGAC
* *
61695070 CCCCTAAACTTT-TTGAAATTGCATTTTCA
1 CCCCTAAACTTTCTTAAAATTACATTTTCA
**
61695099 CCCCTAAACTTTCTTAAAATTACATTTTTG
1 CCCCTAAACTTTCTTAAAATTACATTTTCA
** * * * *
61695129 CCTATCAAC-TTCTTGAAATTATATTTTGA
1 CCCCTAAACTTTCTTAAAATTACATTTTCA
* *
61695158 CCCCTAAATTTTCTCAAAATTA
1 CCCCTAAACTTTCTTAAAATTA
61695180 TGCTTGGCCC
Statistics
Matches: 62, Mismatches: 17, Indels: 3
0.76 0.21 0.04
Matches are distributed among these distances:
29 33 0.53
30 29 0.47
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.42
Consensus pattern (30 bp):
CCCCTAAACTTTCTTAAAATTACATTTTCA
Found at i:61695180 original size:30 final size:30
Alignment explanation
Indices: 61695053--61695180 Score: 91
Period size: 30 Copynumber: 4.3 Consensus size: 30
61695043 ACAAAAAATA
*
61695053 AAAATTTATATTTTGACCCCCTAAACTTT-TT
1 AAAA-TTATATTTTGA-CCCCTAAATTTTCTT
* ** * *
61695084 GAAATTGCATTTTCACCCCTAAACTTTCTT
1 AAAATTATATTTTGACCCCTAAATTTTCTT
* ** * *
61695114 AAAATTACATTTTTG-CCTATCAA-CTTCTT
1 AAAATTATA-TTTTGACCCCTAAATTTTCTT
* *
61695143 GAAATTATATTTTGACCCCTAAATTTTCTC
1 AAAATTATATTTTGACCCCTAAATTTTCTT
61695173 AAAATTAT
1 AAAATTAT
61695181 GCTTGGCCCC
Statistics
Matches: 74, Mismatches: 19, Indels: 9
0.73 0.19 0.09
Matches are distributed among these distances:
28 5 0.07
29 29 0.39
30 33 0.45
31 7 0.09
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (30 bp):
AAAATTATATTTTGACCCCTAAATTTTCTT
Found at i:61695765 original size:13 final size:13
Alignment explanation
Indices: 61695743--61695776 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
61695733 AACCCAAAGG
61695743 AAAAAG-AGAGAA
1 AAAAAGAAGAGAA
61695755 AAAAAGAAGAGAA
1 AAAAAGAAGAGAA
61695768 AAGAAAGAA
1 AA-AAAGAA
61695777 AAGAGGAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 6 0.30
13 8 0.40
14 6 0.30
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAAAGAAGAGAA
Found at i:61695769 original size:22 final size:22
Alignment explanation
Indices: 61695744--61695789 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
61695734 ACCCAAAGGA
*
61695744 AAAAGAGAGAAAAAAAGAAGAG
1 AAAAGAAAGAAAAAAAGAAGAG
* *
61695766 AAAAGAAAGAAAAGAGGAAGAG
1 AAAAGAAAGAAAAAAAGAAGAG
61695788 AA
1 AA
61695790 GGGGAGGCGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (22 bp):
AAAAGAAAGAAAAAAAGAAGAG
Found at i:61695899 original size:19 final size:21
Alignment explanation
Indices: 61695874--61695937 Score: 78
Period size: 23 Copynumber: 3.0 Consensus size: 21
61695864 CCGAGGAAGA
61695874 AGAAG-AAAAAGAAAAAAAAG
1 AGAAGAAAAAAGAAAAAAAAG
61695894 -GAAGAAAAAGAGAGAAGAAAAAG
1 AGAAGAAAAA-AGA-AA-AAAAAG
61695917 AGAAAGAAAAAAGAAAAAAAA
1 AG-AAGAAAAAAGAAAAAAAA
61695938 TAAAAAGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
19 4 0.11
20 4 0.11
21 3 0.08
22 7 0.18
23 8 0.21
24 4 0.11
25 8 0.21
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (21 bp):
AGAAGAAAAAAGAAAAAAAAG
Found at i:61695900 original size:13 final size:12
Alignment explanation
Indices: 61695866--61695927 Score: 61
Period size: 12 Copynumber: 5.0 Consensus size: 12
61695856 GATTCGGCCC
*
61695866 GAGGAAGAAGAA
1 GAGGAAGAAAAA
**
61695878 GAAAAAGAAAAAA
1 GAGGAAG-AAAAA
*
61695891 AAGGAAGAAAAA
1 GAGGAAGAAAAA
61695903 GAGAGAAGAAAAA
1 GAG-GAAGAAAAA
*
61695916 GAGAAAGAAAAA
1 GAGGAAGAAAAA
61695928 AGAAAAAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
12 20 0.50
13 20 0.50
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAGGAAGAAAAA
Found at i:61695910 original size:32 final size:31
Alignment explanation
Indices: 61695870--61695934 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 31
61695860 CGGCCCGAGG
61695870 AAGAAGAAGAAAAAGA-AAA-AAAAGGAAGAAA
1 AAGAAGAAGAAAAAGAGAAAGAAAA--AAGAAA
61695901 AAGAGAGAAGAAAAAGAGAAAGAAAAAAGAAA
1 AAGA-AGAAGAAAAAGAGAAAGAAAAAAGAAA
61695933 AA
1 AA
61695935 AAATAAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
31 4 0.13
32 20 0.65
33 3 0.10
34 4 0.13
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (31 bp):
AAGAAGAAGAAAAAGAGAAAGAAAAAAGAAA
Found at i:61695927 original size:26 final size:23
Alignment explanation
Indices: 61695883--61695937 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 23
61695873 AAGAAGAAAA
*
61695883 AGAAAAAAAAGGAAGAAAAAGAG
1 AGAAAAAAAAGAAAGAAAAAGAG
61695906 AGAAGAAAAAGAGAAAGAAAAA-AG
1 AGAA-AAAAA-AGAAAGAAAAAGAG
61695930 A-AAAAAAA
1 AGAAAAAAA
61695938 TAAAAAGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 5 0.17
23 6 0.21
24 8 0.28
25 10 0.34
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (23 bp):
AGAAAAAAAAGAAAGAAAAAGAG
Found at i:61695928 original size:13 final size:12
Alignment explanation
Indices: 61695870--61695937 Score: 68
Period size: 13 Copynumber: 5.7 Consensus size: 12
61695860 CGGCCCGAGG
* *
61695870 AAGAAGAAGAAA
1 AAGAAAAAGAGA
* *
61695882 AAGAAAAAAAAGG
1 AAG-AAAAAGAGA
61695895 AAGAAAAAGAGA
1 AAGAAAAAGAGA
61695907 GAAGAAAAAGAGA
1 -AAGAAAAAGAGA
61695920 AAGAAAAA-AGA
1 AAGAAAAAGAGA
61695931 AA-AAAAA
1 AAGAAAAA
61695938 TAAAAAGCTA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
10 5 0.10
11 5 0.10
12 18 0.38
13 20 0.42
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (12 bp):
AAGAAAAAGAGA
Found at i:61696144 original size:19 final size:19
Alignment explanation
Indices: 61696099--61696146 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
61696089 AAAAAAAAGG
* *
61696099 CCAGCAGGCCTGTCCAAGC
1 CCAGCAAGCCTGACCAAGC
* * *
61696118 CCAACAAGCCTGACCCAGT
1 CCAGCAAGCCTGACCAAGC
61696137 CCAGCAAGCC
1 CCAGCAAGCC
61696147 CAGAACAGCA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.27, C:0.44, G:0.21, T:0.08
Consensus pattern (19 bp):
CCAGCAAGCCTGACCAAGC
Found at i:61696722 original size:17 final size:17
Alignment explanation
Indices: 61696702--61696779 Score: 75
Period size: 17 Copynumber: 4.4 Consensus size: 17
61696692 TACGGTATTA
61696702 AAAAAAATTCGTGTTTC
1 AAAAAAATTCGTGTTTC
**
61696719 AAAAATTTTCGTGTTTTC
1 AAAAAAATTCGTG-TTTC
61696737 AAAAAAATTGACCGTGTTTC
1 AAAAAAATT---CGTGTTTC
* **
61696757 ATAAATTTTCGTGTTTC
1 AAAAAAATTCGTGTTTC
61696774 AAAAAA
1 AAAAAA
61696780 TCCTCGTGTT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
17 23 0.48
18 11 0.23
20 10 0.21
21 4 0.08
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (17 bp):
AAAAAAATTCGTGTTTC
Found at i:61696744 original size:20 final size:20
Alignment explanation
Indices: 61696719--61696897 Score: 69
Period size: 19 Copynumber: 9.1 Consensus size: 20
61696709 TTCGTGTTTC
61696719 AAAAATTTTCGTGTTTTCAA
1 AAAAATTTTCGTGTTTTCAA
**
61696739 AAAAATTGACCGTG-TTTC--
1 AAAAATT-TTCGTGTTTTCAA
*
61696757 ATAAATTTTCGTG-TTTCAA
1 AAAAATTTTCGTGTTTTCAA
* * *
61696776 AAAATCCTCGTGTTTCGTATTTT-ATC
1 AAAA-----AT-TTTCGTGTTTTCA-A
*
61696802 AAAAATTTT-ATGTTTTCAA
1 AAAAATTTTCGTGTTTTCAA
61696821 AAAAATTTT-GTGTTTT---
1 AAAAATTTTCGTGTTTTCAA
*
61696837 AAAAATTTTCGT-ATTTCAA
1 AAAAATTTTCGTGTTTTCAA
** *
61696856 AAAGAAAATTCGTGTTTCCTAA
1 AAA-AATTTTCGTGTTTTC-AA
*
61696878 AAAAA-TCTCGTG-TTTCAA
1 AAAAATTTTCGTGTTTTCAA
61696896 AA
1 AA
61696898 TTTTTTTTTT
Statistics
Matches: 118, Mismatches: 22, Indels: 40
0.66 0.12 0.22
Matches are distributed among these distances:
16 12 0.10
17 10 0.08
18 10 0.08
19 29 0.25
20 27 0.23
21 10 0.08
22 5 0.04
24 1 0.01
25 7 0.06
26 7 0.06
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.42
Consensus pattern (20 bp):
AAAAATTTTCGTGTTTTCAA
Found at i:61696780 original size:18 final size:17
Alignment explanation
Indices: 61696709--61696778 Score: 77
Period size: 17 Copynumber: 3.9 Consensus size: 17
61696699 TTAAAAAAAA
61696709 TTCGTGTTTCAAAAATT
1 TTCGTGTTTCAAAAATT
61696726 TTCGTGTTTTCAAAAAAATT
1 TTCGTG-TTTC--AAAAATT
** *
61696746 GACCGTGTTTCATAAATT
1 -TTCGTGTTTCAAAAATT
61696764 TTCGTGTTTCAAAAA
1 TTCGTGTTTCAAAAA
61696779 ATCCTCGTGT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
17 18 0.42
18 10 0.23
20 11 0.26
21 4 0.09
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (17 bp):
TTCGTGTTTCAAAAATT
Found at i:61703789 original size:24 final size:23
Alignment explanation
Indices: 61703757--61703848 Score: 132
Period size: 24 Copynumber: 3.9 Consensus size: 23
61703747 TATTATGCCT
* *
61703757 AAAAAA-AAACAAAAAAACAACA
1 AAAAAACAAAAAAAAAAAAAACA
61703779 AAAAAACAAAAAAAACAAAAAACA
1 AAAAAACAAAAAAAA-AAAAAACA
61703803 AAAAAACAAAAAAACAAAAAAACA
1 AAAAAACAAAAAAA-AAAAAAACA
61703827 AAAAAACAAAAAAAAACAAAAA
1 AAAAAACAAAAAAAAA-AAAAA
61703849 AGTAAAAAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
22 6 0.09
23 9 0.14
24 48 0.75
25 1 0.02
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (23 bp):
AAAAAACAAAAAAAAAAAAAACA
Found at i:61703849 original size:8 final size:8
Alignment explanation
Indices: 61703759--61703840 Score: 121
Period size: 8 Copynumber: 9.9 Consensus size: 8
61703749 TTATGCCTAA
61703759 AAAAAAAC
1 AAAAAAAC
61703767 AAAAAAACAAC
1 --AAAAA-AAC
61703778 AAAAAAAC
1 AAAAAAAC
61703786 AAAAAAA-
1 AAAAAAAC
61703793 ACAAAAAAC
1 A-AAAAAAC
61703802 AAAAAAAC
1 AAAAAAAC
61703810 AAAAAAAC
1 AAAAAAAC
61703818 AAAAAAAC
1 AAAAAAAC
61703826 AAAAAAAC
1 AAAAAAAC
61703834 AAAAAAA
1 AAAAAAA
61703841 AACAAAAAAG
Statistics
Matches: 69, Mismatches: 0, Indels: 8
0.90 0.00 0.10
Matches are distributed among these distances:
7 1 0.01
8 54 0.78
9 6 0.09
10 5 0.07
11 3 0.04
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:61703869 original size:1 final size:1
Alignment explanation
Indices: 61703757--61703860 Score: 91
Period size: 1 Copynumber: 104.0 Consensus size: 1
61703747 TATTATGCCT
* * * * * * * *
61703757 AAAAAAAAACAAAAAAACAACAAAAAAACAAAAAAAACAAAAAACAAAAAAACAAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * **
61703822 AAACAAAAAAACAAAAAAAAACAAAAAAGTAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
61703861 GAAGAAAAAT
Statistics
Matches: 78, Mismatches: 25, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 78 1.00
ACGTcount: A:0.88, C:0.11, G:0.01, T:0.01
Consensus pattern (1 bp):
A
Found at i:61705321 original size:83 final size:81
Alignment explanation
Indices: 61704753--61706078 Score: 1546
Period size: 80 Copynumber: 16.5 Consensus size: 81
61704743 TTCTGTTTTC
* * *
61704753 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGGTCGCACACTGAGGTA----TTTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTCTTTTA
*
61704814 AATTTCTGTTTTT-C-G
65 AATTTCTGTTTTTCCAA
*
61704829 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTCTTTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTCTTTTA
* *
61704894 AATTTCTATTTTTCAAAA
65 AATTTCTGTTTTTC-CAA
* * *
61704912 AAAAATCAACTCATATTAC-AGAGATGAGTTGAGCCTCAGGT-CACGCTGAGGTATTTCTTTTAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAGGTATTTCTTTTAA
*
61704975 ATTTCTGTTTTTTTTC-A
66 ATTTCTG--TTTTTCCAA
** * *
61704992 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAAT-CATGCCGAGGTATTTCTTTTAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAGGTATTTCTTTTAA
*
61705056 ATTTCTGTTTTTTCAA
66 ATTTCTGTTTTTCCAA
61705072 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT-CACGCTGAGGTATTTCTTTTAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAGGTATTTCTTTTAA
* *
61705136 ATCTCTGTTTTTCAAA
66 ATTTCTGTTTTTCCAA
*
61705152 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTCTTTTA
* *
61705217 AATTTCTATTTTTCAAAAA
65 AATTTCTGTTTTTC--CAA
* *
61705236 AAAAATCAACTCATATTAC-AGAGGTGAGTTGAGCATCGGGGT-CACGCTGAGGTATTTCTTTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGTCCACGCTGAGGTATTTCTTTTA
61705299 AATTTCTGTTTTTTTTCC-A
65 AATTTCTG---TTTTTCCAA
** *
61705318 AAAAATCAACTCATATTTTGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTCTTTTA
* *
61705383 AATTTCTATTTTTCAAA
65 AATTTCTGTTTTTCCAA
* * *
61705400 AAAAATCAACTCATATTAC-AGAGATGAGTTGAGCCTCTGGT-CACGCTGAGGTATTTCTTTTAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAGGTATTTCTTTTAA
*
61705463 ATTTCTG-GTTT-C--
66 ATTTCTGTTTTTCCAA
*
61705475 AAAAATCAACTCATATTGCGCGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTA----TTTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTCTTTTA
*
61705536 AATTTCTGCTTTT-C-A
65 AATTTCTGTTTTTCCAA
*
61705551 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCGCACGCTGAGGTATTTCTTTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTCTTTTA
61705616 AATTTCTG-TTTT-C--
65 AATTTCTGTTTTTCCAA
*
61705629 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGC-----TATTTC-TTTG
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTCTTTTA
* ** *
61705688 AA--GCTGTAGTTCGCAC
65 AATTTCTGTTTTTC-CAA
****
61705704 CCGGATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGT-CACGCTGAGGTATTTCTTTTAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAGGTATTTCTTTTAA
* *
61705768 ATCTCTGTTTTTCAGAA
66 ATTTCTGTTTTTC-CAA
*
61705785 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTCTTTTA
*
61705850 AATTTCTGTTTTTTCAAA
65 AATTTCTG-TTTTTCCAA
* *
61705868 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCGTTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC-CACGCTGAGGTATTTCTTTTA
* **
61705933 AATTCCTGTTTTTAAAA
65 AATTTCTGTTTTTCCAA
* ** *
61705950 AAAAATCAACTCATAATGCGAGAGGTGAGTTGTATGAGTTGAGTATCGGGTCACATG-TCGAGGT
1 AAAAATCAACTCATATTGC--GA---GAG--G--TGAGTTGAGCCTCGGGTC-CACGCT-GAGGT
61706014 ATTTTCTTTTAAATTTCTGTTTTT-CAA
55 A-TTTCTTTTAAATTTCTGTTTTTCCAA
*
61706041 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
61706079 AGGCCACACG
Statistics
Matches: 1096, Mismatches: 95, Indels: 112
0.84 0.07 0.09
Matches are distributed among these distances:
70 3 0.00
71 2 0.00
72 5 0.00
73 12 0.01
74 13 0.01
75 60 0.05
76 126 0.11
78 69 0.06
79 45 0.04
80 192 0.18
81 115 0.10
82 162 0.15
83 151 0.14
84 62 0.06
85 6 0.01
86 2 0.00
87 2 0.00
89 3 0.00
90 1 0.00
91 45 0.04
92 20 0.02
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (81 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCCACGCTGAGGTATTTCTTTTAA
ATTTCTGTTTTTCCAA
Found at i:61706269 original size:9 final size:9
Alignment explanation
Indices: 61706255--61706288 Score: 52
Period size: 10 Copynumber: 3.8 Consensus size: 9
61706245 GCTTTTTTTA
61706255 AAAAAATAC
1 AAAAAATAC
61706264 AAAAAAATAC
1 -AAAAAATAC
61706274 AAAAAATA-
1 AAAAAATAC
61706282 AAAAAAT
1 AAAAAAT
61706289 TATATTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 7 0.29
9 8 0.33
10 9 0.38
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAATAC
Found at i:61706269 original size:10 final size:10
Alignment explanation
Indices: 61706254--61706287 Score: 54
Period size: 9 Copynumber: 3.6 Consensus size: 10
61706244 TGCTTTTTTT
61706254 AAAAAAATAC
1 AAAAAAATAC
61706264 AAAAAAATAC
1 AAAAAAATAC
61706274 -AAAAAATA-
1 AAAAAAATAC
61706282 AAAAAA
1 AAAAAA
61706288 TTATATTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 13 0.57
10 10 0.43
ACGTcount: A:0.85, C:0.06, G:0.00, T:0.09
Consensus pattern (10 bp):
AAAAAAATAC
Found at i:61706408 original size:30 final size:30
Alignment explanation
Indices: 61706284--61706410 Score: 109
Period size: 30 Copynumber: 4.3 Consensus size: 30
61706274 AAAAAATAAA
61706284 AAAATTATATTTTGACCCCCTAAACTTTT-T
1 AAAATTATATTTTGA-CCCCTAAACTTTTCT
* ** * *
61706314 GAAATTGCATTTTCACCCCTAAACTTTACT
1 AAAATTATATTTTGACCCCTAAACTTTTCT
* * * *
61706344 AAAATTACATTTTTG-CCCATCAACTTCT-T
1 AAAATTATA-TTTTGACCCCTAAACTTTTCT
*
61706373 GAAATTATATTTTGACCCCTAAA-TTTTCT
1 AAAATTATATTTTGACCCCTAAACTTTTCT
61706402 CAAAATTAT
1 -AAAATTAT
61706411 GCTTGGCCCC
Statistics
Matches: 74, Mismatches: 18, Indels: 10
0.73 0.18 0.10
Matches are distributed among these distances:
28 8 0.11
29 27 0.36
30 35 0.47
31 4 0.05
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (30 bp):
AAAATTATATTTTGACCCCTAAACTTTTCT
Found at i:61706993 original size:13 final size:13
Alignment explanation
Indices: 61706971--61707004 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
61706961 AACCCAAAGG
61706971 AAAAAG-AGAGAA
1 AAAAAGAAGAGAA
61706983 AAAAAGAAGAGAA
1 AAAAAGAAGAGAA
61706996 AAGAAAGAA
1 AA-AAAGAA
61707005 AAGAGGAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 6 0.30
13 8 0.40
14 6 0.30
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAAAGAAGAGAA
Found at i:61706997 original size:22 final size:22
Alignment explanation
Indices: 61706972--61707017 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
61706962 ACCCAAAGGA
*
61706972 AAAAGAGAGAAAAAAAGAAGAG
1 AAAAGAAAGAAAAAAAGAAGAG
* *
61706994 AAAAGAAAGAAAAGAGGAAGAG
1 AAAAGAAAGAAAAAAAGAAGAG
61707016 AA
1 AA
61707018 GGGGAGGCGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (22 bp):
AAAAGAAAGAAAAAAAGAAGAG
Found at i:61707127 original size:19 final size:21
Alignment explanation
Indices: 61707102--61707165 Score: 78
Period size: 23 Copynumber: 3.0 Consensus size: 21
61707092 CCGAGGAAGA
61707102 AGAAG-AAAAAGAAAAAAAAG
1 AGAAGAAAAAAGAAAAAAAAG
61707122 -GAAGAAAAAGAGAGAAGAAAAAG
1 AGAAGAAAAA-AGA-AA-AAAAAG
61707145 AGAAAGAAAAAAGAAAAAAAA
1 AG-AAGAAAAAAGAAAAAAAA
61707166 ATAAAAAGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
19 4 0.11
20 4 0.11
21 3 0.08
22 7 0.18
23 8 0.21
24 4 0.11
25 8 0.21
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (21 bp):
AGAAGAAAAAAGAAAAAAAAG
Found at i:61707138 original size:32 final size:31
Alignment explanation
Indices: 61707098--61707162 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 31
61707088 CGGCCCGAGG
61707098 AAGAAGAAGAAAAAGA-AAA-AAAAGGAAGAAA
1 AAGAAGAAGAAAAAGAGAAAGAAAA--AAGAAA
61707129 AAGAGAGAAGAAAAAGAGAAAGAAAAAAGAAA
1 AAGA-AGAAGAAAAAGAGAAAGAAAAAAGAAA
61707161 AA
1 AA
61707163 AAAATAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
31 4 0.13
32 20 0.65
33 3 0.10
34 4 0.13
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (31 bp):
AAGAAGAAGAAAAAGAGAAAGAAAAAAGAAA
Found at i:61707155 original size:26 final size:23
Alignment explanation
Indices: 61707111--61707166 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 23
61707101 AAGAAGAAAA
*
61707111 AGAAAAAAAAGGAAGAAAAAGAG
1 AGAAAAAAAAGAAAGAAAAAGAG
61707134 AGAAGAAAAAGAGAAAGAAAAA-AG
1 AGAA-AAAAA-AGAAAGAAAAAGAG
61707158 A-AAAAAAAA
1 AGAAAAAAAA
61707167 TAAAAAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
21 1 0.03
22 5 0.17
23 6 0.20
24 8 0.27
25 10 0.33
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (23 bp):
AGAAAAAAAAGAAAGAAAAAGAG
Found at i:61707156 original size:13 final size:13
Alignment explanation
Indices: 61707104--61707166 Score: 62
Period size: 13 Copynumber: 5.1 Consensus size: 13
61707094 GAGGAAGAAG
*
61707104 AAGAAAAAGAAAA
1 AAGAGAAAGAAAA
* *
61707117 AAAAGGAAG-AAA
1 AAGAGAAAGAAAA
61707129 AAGAGAGAAG-AAA
1 AAGAGA-AAGAAAA
61707142 AAGAGAAAGAAAA
1 AAGAGAAAGAAAA
61707155 AAGA-AAA-AAAA
1 AAGAGAAAGAAAA
61707166 A
1 A
61707167 TAAAAAGCTA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
11 5 0.12
12 13 0.30
13 25 0.58
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAGAGAAAGAAAA
Found at i:61707161 original size:6 final size:6
Alignment explanation
Indices: 61707098--61707166 Score: 61
Period size: 6 Copynumber: 11.2 Consensus size: 6
61707088 CGGCCCGAGG
* * *
61707098 AAGAAG AAGAAA AAGAAA AA-AAA GGAAGAAA AAGAGAG AAGAAA AAGAGA
1 AAGAAA AAGAAA AAGAAA AAGAAA --AAGAAA AAGA-AA AAGAAA AAGAAA
61707148 AAGAAAA AAGAAA AA-AAA A
1 AAG-AAA AAGAAA AAGAAA A
61707167 TAAAAAGCTA
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
5 7 0.13
6 31 0.58
7 12 0.23
8 3 0.06
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:61707165 original size:11 final size:11
Alignment explanation
Indices: 61707107--61707166 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
61707097 GAAGAAGAAG
61707107 AAAAAGAAAAA
1 AAAAAGAAAAA
61707118 AAAGGAAG-AAAA
1 AAA--AAGAAAAA
* * *
61707130 AGAGAGAAGAA
1 AAAAAGAAAAA
* *
61707141 AAAGAGAAAGA
1 AAAAAGAAAAA
61707152 AAAAAGAAAAA
1 AAAAAGAAAAA
61707163 AAAA
1 AAAA
61707167 TAAAAAGCTA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
10 2 0.05
11 27 0.71
12 6 0.16
13 3 0.08
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Done.