Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008602.1 Hibiscus syriacus cultivar Beakdansim tig00111557_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: 277273
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4201 original size:30 final size:32
Alignment explanation
Indices: 4146--4207 Score: 92
Period size: 30 Copynumber: 2.0 Consensus size: 32
4136 ACAGTATACA
*
4146 AAATAAATGTGTAAGACCATCTAAACAGACGC
1 AAATAAATGTGTAAGACCAGCTAAACAGACGC
*
4178 AAAT-AATGTG-AAGATCAGCTAAACAGACGC
1 AAATAAATGTGTAAGACCAGCTAAACAGACGC
4208 TAATCGGGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 18 0.64
31 6 0.21
32 4 0.14
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.18
Consensus pattern (32 bp):
AAATAAATGTGTAAGACCAGCTAAACAGACGC
Found at i:6191 original size:24 final size:23
Alignment explanation
Indices: 6164--6220 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
6154 TTTATAAAAT
6164 AAATAAATAATCTGTTTGAAGTTA
1 AAATAAATAATCT-TTTGAAGTTA
* *
6188 AAATAAATCAA-CTTTTTAATTTA
1 AAATAAAT-AATCTTTTGAAGTTA
6211 AAAT-AATAAT
1 AAATAAATAAT
6221 TTATTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 2 0.07
22 3 0.10
23 12 0.41
24 10 0.34
25 2 0.07
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (23 bp):
AAATAAATAATCTTTTGAAGTTA
Found at i:6234 original size:25 final size:25
Alignment explanation
Indices: 6200--6272 Score: 109
Period size: 25 Copynumber: 3.1 Consensus size: 25
6190 ATAAATCAAC
6200 TTTTTAATTTAAAATAATAATTTAT
1 TTTTTAATTTAAAATAATAATTTAT
*
6225 TTTTTAATTTAAAATTATAATTTAT
1 TTTTTAATTTAAAATAATAATTTAT
6250 TTTTTAA--T-AAATAAT-ATTTAT
1 TTTTTAATTTAAAATAATAATTTAT
6271 TT
1 TT
6273 ATATACATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.17
22 6 0.13
23 1 0.02
25 31 0.67
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTTTAATTTAAAATAATAATTTAT
Found at i:6267 original size:17 final size:19
Alignment explanation
Indices: 6247--6286 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
6237 AATTATAATT
6247 TATTT-TTTA-ATAAATAA
1 TATTTATTTATATAAATAA
*
6264 TATTTATTTATATACATAA
1 TATTTATTTATATAAATAA
6283 -ATTT
1 TATTT
6287 GCATATATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 5 0.25
18 8 0.40
19 7 0.35
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTTATTTATATAAATAA
Found at i:6777 original size:35 final size:35
Alignment explanation
Indices: 6730--6841 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 35
6720 AAAACATTCC
* *
6730 TCAATTTTATTCTAAACCCCAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* *
6765 TCAATTTCATTCTAAACCCTAAATTACAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* * * *
6800 TCAATTACATTCTAAAACCCAAATTCTAAAATATT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
6835 TCAATTT
1 TCAATTT
6842 AAGGAGGAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 66 1.00
ACGTcount: A:0.43, C:0.21, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:7943 original size:34 final size:33
Alignment explanation
Indices: 7890--7998 Score: 130
Period size: 34 Copynumber: 3.2 Consensus size: 33
7880 TAAAAAGACA
* *
7890 AAATT-AAGTATTTTAGAATTTGGTTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGG-TTTAGAATG
*
7923 TAATTGAATTATTTTGGAATTTAGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTT-GGTTTAGAATG
* *
7957 AAATTGAATTACTTTGGAATTTGTGGTTTGGAATG
1 AAATTGAATTATTTTGGAA-TT-TGGTTTAGAATG
7992 AAATTGA
1 AAATTGA
7999 GGATTGTTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
33 4 0.06
34 40 0.61
35 21 0.32
36 1 0.02
ACGTcount: A:0.34, C:0.01, G:0.21, T:0.44
Consensus pattern (33 bp):
AAATTGAATTATTTTGGAATTTGGTTTAGAATG
Found at i:7992 original size:35 final size:34
Alignment explanation
Indices: 7905--7998 Score: 134
Period size: 34 Copynumber: 2.7 Consensus size: 34
7895 AAGTATTTTA
* * *
7905 GAATTTGGTTTTAGAATGTAATTGAATTATTTTG
1 GAATTTGGGTTTAGAATGAAATTGAATTACTTTG
*
7939 GAATTTAGGTTTAGAATGAAATTGAATTACTTTG
1 GAATTTGGGTTTAGAATGAAATTGAATTACTTTG
*
7973 GAATTTGTGGTTTGGAATGAAATTGA
1 GAATTTG-GGTTTAGAATGAAATTGA
7999 GGATTGTTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 36 0.68
35 17 0.32
ACGTcount: A:0.32, C:0.01, G:0.23, T:0.44
Consensus pattern (34 bp):
GAATTTGGGTTTAGAATGAAATTGAATTACTTTG
Found at i:9965 original size:2 final size:2
Alignment explanation
Indices: 9954--9991 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
9944 TATCTATTTT
9954 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9992 TACCCTCTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13251 original size:60 final size:60
Alignment explanation
Indices: 13156--13310 Score: 167
Period size: 60 Copynumber: 2.6 Consensus size: 60
13146 TTTGGATACG
* * * * *
13156 AAATTAGAAA-ATTCAAAAATTTGAAGACTGA-TTTAAAATAAA-ATTTATAGTTTGGGGATG
1 AAATTA-AAATATTCAAAAATTT-AAGAATCATTTTAAAA-AAAGATTAATAGTTTGAGGATA
*
13216 AAATTGAAAAT-TTCAAAACTTTAAGGAAT-ATTTTAAAAAAAGATTAATAGTTTGAGGATA
1 AAATT-AAAATATTCAAAAATTTAA-GAATCATTTTAAAAAAAGATTAATAGTTTGAGGATA
*
13276 AAATTAAAATATTTAAAAATTTAAGAATCATTTTA
1 AAATTAAAATATTCAAAAATTTAAGAATCATTTTA
13311 GAATGAAAGT
Statistics
Matches: 81, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
59 15 0.19
60 65 0.80
61 1 0.01
ACGTcount: A:0.50, C:0.03, G:0.12, T:0.35
Consensus pattern (60 bp):
AAATTAAAATATTCAAAAATTTAAGAATCATTTTAAAAAAAGATTAATAGTTTGAGGATA
Found at i:13441 original size:16 final size:17
Alignment explanation
Indices: 13411--13445 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
13401 AATTTTATTT
13411 TTTTAAAAATTTAAATCA
1 TTTTAAAAA-TTAAATCA
13429 TTTTAAAAA-TAAATCA
1 TTTTAAAAATTAAATCA
13445 T
1 T
13446 AAGGTAGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (17 bp):
TTTTAAAAATTAAATCA
Found at i:23580 original size:2 final size:2
Alignment explanation
Indices: 23575--23612 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
23565 AGTGTGTAGT
23575 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
23613 ACATAAGTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27292 original size:20 final size:21
Alignment explanation
Indices: 27267--27316 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
27257 TTATTCCACT
*
27267 AATTAAATA-AATAATAAACA
1 AATTAAATATAATAATAAAAA
*
27287 AATTAAA-ATAATACTAAAAA
1 AATTAAATATAATAATAAAAA
*
27307 AATAAAATAT
1 AATTAAATAT
27317 TCACAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 22 0.88
21 2 0.08
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (21 bp):
AATTAAATATAATAATAAAAA
Found at i:27624 original size:4 final size:4
Alignment explanation
Indices: 27615--27652 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
27605 GGTATTTATA
*
27615 GGAG GGAG GGAG GGAG GGAG GGAG AGG-G AGAG GGAG GG
1 GGAG GGAG GGAG GGAG GGAG GGAG -GGAG GGAG GGAG GG
27653 GGATGGGCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 1 0.03
4 27 0.90
5 2 0.07
ACGTcount: A:0.26, C:0.00, G:0.74, T:0.00
Consensus pattern (4 bp):
GGAG
Found at i:33661 original size:6 final size:6
Alignment explanation
Indices: 33650--33690 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
33640 TTATTGAGGG
33650 TGGCAC TGGCAC TGGCAC TGGCAC TGGCAC TGGCAC TGGCA
1 TGGCAC TGGCAC TGGCAC TGGCAC TGGCAC TGGCAC TGGCA
33691 GCCTGCCAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.17, C:0.32, G:0.34, T:0.17
Consensus pattern (6 bp):
TGGCAC
Found at i:33822 original size:15 final size:15
Alignment explanation
Indices: 33791--33835 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
33781 AACTATAGTT
33791 TAATGAATACA-TTTA
1 TAAT-AATACATTTTA
*
33806 TATTAATACATTTTA
1 TAATAATACATTTTA
*
33821 TAATATTACATTTTA
1 TAATAATACATTTTA
33836 GTTTCGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 6 0.23
15 20 0.77
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (15 bp):
TAATAATACATTTTA
Found at i:38148 original size:21 final size:21
Alignment explanation
Indices: 38115--38166 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
38105 CCAGAATGAT
* *
38115 AACTTCTCAAATAAAACAATG
1 AACTCCTCCAATAAAACAATG
38136 AACTCCTCCAATAAAACAATG
1 AACTCCTCCAATAAAACAATG
38157 AACTCCTCCA
1 AACTCCTCCA
38167 GATGTCCAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.46, C:0.29, G:0.04, T:0.21
Consensus pattern (21 bp):
AACTCCTCCAATAAAACAATG
Found at i:44110 original size:2 final size:2
Alignment explanation
Indices: 44103--44135 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
44093 TTTACAAACT
44103 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 T
44136 TTTAAATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45389 original size:21 final size:21
Alignment explanation
Indices: 45365--45408 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
45355 CAAACTTACA
45365 TGATAA-TCTACAATATTGATG
1 TGATAATTCT-CAATATTGATG
*
45386 TGATAATTCTCAATATTGTTG
1 TGATAATTCTCAATATTGATG
45407 TG
1 TG
45409 GCAATACTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (21 bp):
TGATAATTCTCAATATTGATG
Found at i:51908 original size:64 final size:64
Alignment explanation
Indices: 51839--52075 Score: 264
Period size: 63 Copynumber: 3.7 Consensus size: 64
51829 TAAAGATGAC
** *
51839 TGGTTTACAAGTTGCCTTCACCATTCATATTTATTATTTTAAAAAAAGATACAATGAAGATGGT
1 TGGTTTACAAGCCGCCTTCACTATTCATATTTATTATTTTAAAAAAAGATACAATGAAGATGGT
** * * **
51903 TGGTTTACAAGCCATCTTCACTATTAATATTTATTATTTT-AAAATATCTACAATGAAGATGGT
1 TGGTTTACAAGCCGCCTTCACTATTCATATTTATTATTTTAAAAAAAGATACAATGAAGATGGT
** * * * * *
51966 TGGTTTACAAGCCGTTTTTTACTATTCATATTTATTA--TTAAAAAAGGATAGAGTGAAGATGAT
1 TGGTTTACAAGCCG-CCTTCACTATTCATATTTATTATTTTAAAAAAAGATACAATGAAGATGGT
* * * *
52029 TGGTTTAGAAGCCTCCTTTACTATTCATATTTACTATTTTAAAAAAA
1 TGGTTTACAAGCCGCCTTCACTATTCATATTTATTATTTTAAAAAAA
52076 TAATTGCTCG
Statistics
Matches: 143, Mismatches: 26, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
62 21 0.15
63 61 0.43
64 61 0.43
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (64 bp):
TGGTTTACAAGCCGCCTTCACTATTCATATTTATTATTTTAAAAAAAGATACAATGAAGATGGT
Found at i:52253 original size:64 final size:63
Alignment explanation
Indices: 52118--52273 Score: 165
Period size: 64 Copynumber: 2.5 Consensus size: 63
52108 GCGAGGATTG
* * *
52118 CTGGTTTACAAACCG-CTTTCACTA-TCATATTTATTATTTAAAAAAAGTTATAGTGAAGATGG
1 CTGGTTTACAAACCGCCTTT-ACTATTCATATTTACTATTTAAAAAAAGCTATAGTGAAGATGA
* * * * *
52180 TTGGTTTACAAGCTGCCTTTACTATTCATATTTACTATTTTAAAAAAAGCTA-CGCTGAATATGA
1 CTGGTTTACAAACCGCCTTTACTATTCATATTTACTA-TTTAAAAAAAGCTATAG-TGAAGATGA
* * *
52244 CTGGTTTACAACCCGCCATCACTATTCATA
1 CTGGTTTACAAACCGCCTTTACTATTCATA
52274 AAAAAATTGT
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
62 16 0.21
63 16 0.21
64 45 0.58
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.37
Consensus pattern (63 bp):
CTGGTTTACAAACCGCCTTTACTATTCATATTTACTATTTAAAAAAAGCTATAGTGAAGATGA
Found at i:55340 original size:14 final size:14
Alignment explanation
Indices: 55302--55345 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
55292 TAAAAACTTA
55302 AATTAA-TTAAT-T
1 AATTAATTTAATAT
55314 AATTAATTATAATAT
1 AATTAATT-TAATAT
*
55329 ATTTAATTTAATAT
1 AATTAATTTAATAT
55343 AAT
1 AAT
55346 ATTTATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 6 0.22
13 1 0.04
14 12 0.44
15 8 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTAATTTAATAT
Found at i:60609 original size:2 final size:2
Alignment explanation
Indices: 60604--60634 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
60594 ATTATAAGGA
60604 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
60635 ATTTAAAATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:61005 original size:24 final size:24
Alignment explanation
Indices: 60978--61024 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
60968 GATAAAATTC
*
60978 ATCATAGGTCC-ATAAATTATTTTA
1 ATCATAGG-CCAACAAATTATTTTA
61002 ATCATAGGCCAACAAATTATTTT
1 ATCATAGGCCAACAAATTATTTT
61025 TAAGCATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (24 bp):
ATCATAGGCCAACAAATTATTTTA
Found at i:61067 original size:20 final size:19
Alignment explanation
Indices: 61042--61085 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
61032 TAACTTTTTA
61042 AAAATTATAAAATAATTATT
1 AAAATTATAAAATAATTA-T
* *
61062 AAAATTATGAAATGATTAT
1 AAAATTATAAAATAATTAT
61081 AAAAT
1 AAAAT
61086 AATCATTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (19 bp):
AAAATTATAAAATAATTAT
Found at i:61566 original size:59 final size:55
Alignment explanation
Indices: 61463--61585 Score: 133
Period size: 58 Copynumber: 2.1 Consensus size: 55
61453 GACCATTTTG
* *
61463 TAACTTTTAATAGTCGAGGGACTTAAAAAATAATGTCTCATAGTTAGGGGATCATTGA
1 TAACTTTTAATAGTC-AGGGACTCAAAAAATAATATCTCATAGTT--GGGATCATTGA
*
61521 TAACTTTTAATAGT-AGGATGACTCAATAAAATAATATC-CTATAGTTGGGATCATTTA
1 TAACTTTTAATAGTCAGG--GACTCAA-AAAATAATATCTC-ATAGTTGGGATCATTGA
61578 TATACTTT
1 TA-ACTTT
61586 ACCTCGATTT
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
56 3 0.05
57 12 0.21
58 26 0.46
59 16 0.28
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (55 bp):
TAACTTTTAATAGTCAGGGACTCAAAAAATAATATCTCATAGTTGGGATCATTGA
Found at i:67626 original size:25 final size:27
Alignment explanation
Indices: 67582--67641 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
67572 ATGACAAGGC
67582 GAATCA-TCAGGTTCAACAGC-CAC-AG
1 GAATCACTCAGGTTC-ACAGCTCACGAG
67607 GAATCACTACAGGTTC-CAGCTCACGAG
1 GAATCACT-CAGGTTCACAGCTCACGAG
*
67634 GAACCACT
1 GAATCACT
67642 GGTGGCTTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 10 0.33
26 4 0.13
27 16 0.53
ACGTcount: A:0.33, C:0.30, G:0.20, T:0.17
Consensus pattern (27 bp):
GAATCACTCAGGTTCACAGCTCACGAG
Found at i:70983 original size:4 final size:4
Alignment explanation
Indices: 70974--70998 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
70964 TTTAAATAGT
70974 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
70999 GGGCTGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:71672 original size:183 final size:183
Alignment explanation
Indices: 71364--71730 Score: 617
Period size: 183 Copynumber: 2.0 Consensus size: 183
71354 ATCATATCAC
* *
71364 AATTAACGGATTAATATTCAACTCAGAATATCGTCTATTTTTTAGCGAAAAATGATGAGTTTAGA
1 AATTAACGGATTAATATTCAAATCAGAATATCGTCTATTTTTTAGCGAAAAATGACGAGTTTAGA
*
71429 ATATAATGAATAGTCGAATGACAATATTGTAACTTTTAATAATCAAACGAATTAACAAAGCAACA
66 ATATAATGAATAGTCGAATGACAATATTGTAACTTTTAATAATCAAACGAATCAACAAAGCAACA
*
71494 CTATATAATCAGAGTAGCATTCTGTAATTTTTAATAATTGAAGAACTTAATAA
131 CTATATAATCAGAGTAGCATTCTGTAACTTTTAATAATTGAAGAACTTAATAA
* *
71547 AATTAACGGATTAATATTCAAATCAGAATATCGTCTATTTTTTAGCGGAAAATGACGAGTTTGGA
1 AATTAACGGATTAATATTCAAATCAGAATATCGTCTATTTTTTAGCGAAAAATGACGAGTTTAGA
* * * *
71612 ATATAATGAATAGTCGAATGACAATCTTGTAACTTTTAATGATCAAACGACTCAACAAAGCAACG
66 ATATAATGAATAGTCGAATGACAATATTGTAACTTTTAATAATCAAACGAATCAACAAAGCAACA
* * *
71677 TTATATAATCAGAGTAGCATTTTTTAACTTTTAATAATTGAAGAACTTAATAA
131 CTATATAATCAGAGTAGCATTCTGTAACTTTTAATAATTGAAGAACTTAATAA
71730 A
1 A
71731 TTAGTATCCT
Statistics
Matches: 171, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
183 171 1.00
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.33
Consensus pattern (183 bp):
AATTAACGGATTAATATTCAAATCAGAATATCGTCTATTTTTTAGCGAAAAATGACGAGTTTAGA
ATATAATGAATAGTCGAATGACAATATTGTAACTTTTAATAATCAAACGAATCAACAAAGCAACA
CTATATAATCAGAGTAGCATTCTGTAACTTTTAATAATTGAAGAACTTAATAA
Found at i:83312 original size:90 final size:91
Alignment explanation
Indices: 83198--83380 Score: 350
Period size: 91 Copynumber: 2.0 Consensus size: 91
83188 AAGAGGTCCC
*
83198 TGTTGGGCCCTTTTTGTATTTTTTTTTAAATTAGAAACAA-TTTTATATACATAAAATTGAATTC
1 TGTTGGGCCCTTTTTGTATTTTTTTTTAAATTAGAAACAATTTTTATATACATAAAATTGAATCC
83262 TTTAGGAATTGAGTCTATATCTCAAG
66 TTTAGGAATTGAGTCTATATCTCAAG
83288 TGTTGGGCCCTTTTTGTATTTTTTTTTAAATTAGAAACAATTTTTATATACATAAAATTGAATCC
1 TGTTGGGCCCTTTTTGTATTTTTTTTTAAATTAGAAACAATTTTTATATACATAAAATTGAATCC
83353 TTTAGGAATTGAGTCTATATCTCAAG
66 TTTAGGAATTGAGTCTATATCTCAAG
83379 TG
1 TG
83381 GTAGAGCATA
Statistics
Matches: 91, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
90 40 0.44
91 51 0.56
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (91 bp):
TGTTGGGCCCTTTTTGTATTTTTTTTTAAATTAGAAACAATTTTTATATACATAAAATTGAATCC
TTTAGGAATTGAGTCTATATCTCAAG
Found at i:87591 original size:14 final size:14
Alignment explanation
Indices: 87569--87617 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
87559 GTTTTTTATC
*
87569 AAAAGTAAAATATT
1 AAAATTAAAATATT
87583 AAAATTAAAATATTT
1 AAAATTAAAATA-TT
87598 AAAA--AAAATA--
1 AAAATTAAAATATT
87608 AAAATTAAAA
1 AAAATTAAAA
87618 AAATTATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
10 4 0.13
12 4 0.13
13 6 0.19
14 11 0.35
15 6 0.19
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (14 bp):
AAAATTAAAATATT
Found at i:87618 original size:17 final size:18
Alignment explanation
Indices: 87583--87620 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
87573 GTAAAATATT
* *
87583 AAAATTAAAATATTTAAA
1 AAAAATAAAATATTAAAA
87601 AAAAATAAAA-ATTAAAA
1 AAAAATAAAATATTAAAA
87618 AAA
1 AAA
87621 TTATTTAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAAATAAAATATTAAAA
Found at i:88046 original size:26 final size:26
Alignment explanation
Indices: 87985--88046 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
87975 TATCAATTTA
87985 ATTT-TAAAAATAATATATAACAATT
1 ATTTATAAAAATAATATATAACAATT
* *
88010 ATTCA-ATAAAATAATATATAATTAA-T
1 ATTTATA-AAAATAATATATAA-CAATT
88036 ATTTATAAAAA
1 ATTTATAAAAA
88047 ATCATTTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
25 4 0.13
26 23 0.77
27 3 0.10
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (26 bp):
ATTTATAAAAATAATATATAACAATT
Found at i:88460 original size:84 final size:83
Alignment explanation
Indices: 88323--88488 Score: 242
Period size: 84 Copynumber: 2.0 Consensus size: 83
88313 ATATTACTTT
**
88323 CCATAATTTTTTAGATAAATTATAACAGTGATCACCTAACTATTTTTCATTTTTATTTTGATCAC
1 CCATAATTTTTTAGATAAATTATAACAGTGATCACCTAACTATTGCTCATTTTTATTTTGATCAC
88388 CATATTTGAAATTTTACC
66 CATATTTGAAATTTTACC
* * * * *
88406 CCATAAATTTTTTGGATAAATTATAATAGTGATCCCCTAATTATTGCTCCTTTTTATTTTGATCA
1 CCAT-AATTTTTTAGATAAATTATAACAGTGATCACCTAACTATTGCTCATTTTTATTTTGATCA
* *
88471 CTATTTTTGAAATTTTAC
65 CCATATTTGAAATTTTAC
88489 AAATTAGGTC
Statistics
Matches: 73, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
83 4 0.05
84 69 0.95
ACGTcount: A:0.31, C:0.15, G:0.07, T:0.47
Consensus pattern (83 bp):
CCATAATTTTTTAGATAAATTATAACAGTGATCACCTAACTATTGCTCATTTTTATTTTGATCAC
CATATTTGAAATTTTACC
Found at i:88836 original size:18 final size:19
Alignment explanation
Indices: 88800--88837 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
88790 TGCTACAAAC
88800 AATTATTATATTTTCTAAA
1 AATTATTATATTTTCTAAA
88819 AATTA-TATAATTTT-TAAA
1 AATTATTAT-ATTTTCTAAA
88837 A
1 A
88838 TCAAACAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
AATTATTATATTTTCTAAA
Found at i:92296 original size:22 final size:18
Alignment explanation
Indices: 92248--92322 Score: 87
Period size: 18 Copynumber: 3.9 Consensus size: 18
92238 TCAGTATTTA
92248 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
*
92266 TCCCAAAGGACCACTGGATACG
1 TCCCGAAGGACCACT--AT--G
92288 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
**
92306 TCCCGAATAACCACTAT
1 TCCCGAAGGACCACTAT
92323 ACTCTCGACT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
18 30 0.61
20 4 0.08
22 15 0.31
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:95320 original size:37 final size:37
Alignment explanation
Indices: 95252--95343 Score: 116
Period size: 37 Copynumber: 2.5 Consensus size: 37
95242 TTTTATTATT
*
95252 TCGGGTCGGGTCGGG-TTTTTAATTCATATATTCGAG
1 TCGGGTCGGGTCGGGTTTTTTAAGTCATATATTCGAG
* * *
95288 TCGGGTTGGGTCGGGTTTTTTAAGT-GTGATATTCGGG
1 TCGGGTCGGGTCGGGTTTTTTAAGTCAT-ATATTCGAG
95325 TCGGGTCGGGTTCGGGTTT
1 TCGGGTCGGG-TCGGGTTT
95344 AGGGTGAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
36 15 0.31
37 25 0.52
38 8 0.17
ACGTcount: A:0.11, C:0.12, G:0.38, T:0.39
Consensus pattern (37 bp):
TCGGGTCGGGTCGGGTTTTTTAAGTCATATATTCGAG
Found at i:95479 original size:233 final size:235
Alignment explanation
Indices: 95053--95531 Score: 750
Period size: 233 Copynumber: 2.0 Consensus size: 235
95043 TTTATTTTGT
*
95053 TCGGGTCGGGTCGATTTTTTTAAGTGTGATATTCGGGTCGGGTCGAATTCGGGTTTAGGGTGAAA
1 TCGGGTCGGGTCGAGTTTTTTAAGTGTGATATTCGGGTCGGGTCGAATTCGGGTTTAGGGTGAAA
* * *
95118 ATTACCTGACCCGACCCGAAAATATATATAATTTTATCTTATATATTTAGGAATAATTACAATAA
66 AATACCTGACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAA
**
95183 TACCCCTCTATATATAATTTTTTTCAATTAAGTCATTGTTTTTATTGAATAAAAATATTTTTTAT
131 TACCCCTCTATATATAATTTTTTTCAATTAAGTCACCGTTTTTATTGAATAAAAATATTTTTTAT
* ** *
95248 TATTTCGGGTCGGGTCGGGTTTTTAATTCATATATTCGAG
196 TATTTCGGCTAAGGTCGGGTTTCTAATTCATATATTCGAG
* * **
95288 TCGGGTTGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAA
1 TCGGGTCGGGTCGAGTTTTTTAAGTGTGATATTCGGGTCGGGTCGAATTCGGGTTTAGGGTGAAA
*
95353 AATACCCT-ACCCGA-CC-AAAAAATATATAATTTTGCCTTATATATTTAGGAATAATTACAATA
66 AATA-CCTGACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATA
95415 ATACCCCTCTATATATAA-TTTTTTCAATTAAGTCACCGTTTTTATTGAATAAAAATATTTTTTT
130 ATACCCCTCTATATATAATTTTTTTCAATTAAGTCACCGTTTTTATTGAATAAAAATA-TTTTTT
* *
95479 ATTATTTCGGCTAAGGTCGGGTTTCTAATTTATATATTCGGG
194 ATTATTTCGGCTAAGGTCGGGTTTCTAATTCATATATTCGAG
*
95521 TCAGGTCGGGT
1 TCGGGTCGGGT
95532 GAAACTTTAT
Statistics
Matches: 223, Mismatches: 19, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
232 37 0.17
233 112 0.50
234 2 0.01
235 69 0.31
236 3 0.01
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (235 bp):
TCGGGTCGGGTCGAGTTTTTTAAGTGTGATATTCGGGTCGGGTCGAATTCGGGTTTAGGGTGAAA
AATACCTGACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAA
TACCCCTCTATATATAATTTTTTTCAATTAAGTCACCGTTTTTATTGAATAAAAATATTTTTTAT
TATTTCGGCTAAGGTCGGGTTTCTAATTCATATATTCGAG
Found at i:96889 original size:29 final size:29
Alignment explanation
Indices: 96828--96889 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
96818 TTTTTTCTCT
* * * *
96828 TTTATTTTATTCATTGTATTTTTAATTTT
1 TTTAATTTATTCATTGTACTTTTAAATTG
96857 TTTAATTTATTCATT-TAACTTTTAAATTG
1 TTTAATTTATTCATTGT-ACTTTTAAATTG
96886 TTTA
1 TTTA
96890 TGATTGGATC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (29 bp):
TTTAATTTATTCATTGTACTTTTAAATTG
Found at i:97834 original size:12 final size:13
Alignment explanation
Indices: 97804--97833 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
97794 CACGTTCAAT
97804 TTTTTAAAAAATA
1 TTTTTAAAAAATA
*
97817 TTTTTAAATAATA
1 TTTTTAAAAAATA
97830 TTTT
1 TTTT
97834 ATTTTTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTTTAAAAAATA
Found at i:97960 original size:16 final size:15
Alignment explanation
Indices: 97935--97964 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
97925 AGATACTATT
97935 TTTAACAAAAAATTA
1 TTTAACAAAAAATTA
97950 TTTAGACAAAAAATT
1 TTTA-ACAAAAAATT
97965 TTAAGATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (15 bp):
TTTAACAAAAAATTA
Found at i:101442 original size:22 final size:22
Alignment explanation
Indices: 101393--101445 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
101383 TTGTTTAAAG
101393 TTTTTTTTATCTTAATTGAAAA
1 TTTTTTTTATCTTAATTGAAAA
**
101415 AGTTTTTTATCTTAATTG-AAA
1 TTTTTTTTATCTTAATTGAAAA
101436 TTTTTTTTAT
1 TTTTTTTTAT
101446 TCAAATAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.28, C:0.04, G:0.06, T:0.62
Consensus pattern (22 bp):
TTTTTTTTATCTTAATTGAAAA
Found at i:113266 original size:30 final size:31
Alignment explanation
Indices: 113208--113267 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
113198 CAGTTACATT
*
113208 GGGGACCATATTGCAAACGGACTAAATGTTG
1 GGGGACCATATTGCAAACAGACTAAATGTTG
*
113239 GGGGACTATATTGCAAACAGACT-AATGTT
1 GGGGACCATATTGCAAACAGACTAAATGTT
113268 AGGAGATTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 6 0.22
31 21 0.78
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (31 bp):
GGGGACCATATTGCAAACAGACTAAATGTTG
Found at i:113281 original size:30 final size:31
Alignment explanation
Indices: 113215--113284 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
113205 ATTGGGGACC
* * *
113215 ATATTGCAAACGGACTAAATGTTGGGGGACT
1 ATATTGCAAACAGACTAAATGTTAGGAGACT
*
113246 ATATTGCAAACAGACT-AATGTTAGGAGATT
1 ATATTGCAAACAGACTAAATGTTAGGAGACT
*
113276 GTATTGCAA
1 ATATTGCAA
113285 GTTTTAAAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 19 0.56
31 15 0.44
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (31 bp):
ATATTGCAAACAGACTAAATGTTAGGAGACT
Found at i:114366 original size:27 final size:30
Alignment explanation
Indices: 114336--114395 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 30
114326 TATGGTCTCC
114336 AACAG-TT-ACGTTGGG-GACCATATTGCA
1 AACAGATTAACGTTGGGAGACCATATTGCA
* *
114363 AACAGATTAGATGTTGGGAGACTATATTGCA
1 AACAGATTA-ACGTTGGGAGACCATATTGCA
114394 AA
1 AA
114396 TGGACTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 5 0.19
28 2 0.07
30 7 0.26
31 13 0.48
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (30 bp):
AACAGATTAACGTTGGGAGACCATATTGCA
Found at i:114391 original size:31 final size:30
Alignment explanation
Indices: 114345--114424 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 30
114335 CAACAGTTAC
* * *
114345 GTTGGGGACCATATTGCAAACAGATTAGAT
1 GTTGGGGACTATATTGCAAACAGACTAAAT
**
114375 GTTGGGAGACTATATTGCAAATGGACTAAAT
1 GTTGGG-GACTATATTGCAAACAGACTAAAT
*
114406 GTTGGGGACTGTATTGCAA
1 GTTGGGGACTATATTGCAA
114425 GTTTTAAAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 18 0.42
31 25 0.58
ACGTcount: A:0.31, C:0.11, G:0.29, T:0.29
Consensus pattern (30 bp):
GTTGGGGACTATATTGCAAACAGACTAAAT
Found at i:116714 original size:35 final size:34
Alignment explanation
Indices: 116667--116733 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 34
116657 TTTGCCTAAA
116667 CAAAACTCCATTGTAAAGGCCGATAAAACTAGAAT
1 CAAAACTCCATTGTAAAGGCCGAT-AAACTAGAAT
* *
116702 CAAAACTTCATTGTAAAGGCTGATAAACTAGA
1 CAAAACTCCATTGTAAAGGCCGATAAACTAGA
116734 TTCCTTCTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 8 0.27
35 22 0.73
ACGTcount: A:0.45, C:0.18, G:0.15, T:0.22
Consensus pattern (34 bp):
CAAAACTCCATTGTAAAGGCCGATAAACTAGAAT
Found at i:126409 original size:2 final size:2
Alignment explanation
Indices: 126402--126427 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
126392 ACTGTTGTTA
126402 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
126428 TTGAATTGAA
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:128319 original size:12 final size:12
Alignment explanation
Indices: 128294--128362 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
128284 ACGGAGATAT
* *
128294 CAGAAATCAAAA
1 CAGAATTCAGAA
128306 CAGAATTCAGAA
1 CAGAATTCAGAA
*
128318 C--AATATCATAA
1 CAGAAT-TCAGAA
* *
128329 CAGAATCCAGAT
1 CAGAATTCAGAA
*
128341 CAGAAATCAGAA
1 CAGAATTCAGAA
*
128353 CAAAATTCAG
1 CAGAATTCAG
128363 GTCATATATC
Statistics
Matches: 43, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
10 3 0.07
11 6 0.14
12 31 0.72
13 3 0.07
ACGTcount: A:0.54, C:0.19, G:0.12, T:0.16
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:128354 original size:24 final size:24
Alignment explanation
Indices: 128292--128385 Score: 91
Period size: 24 Copynumber: 4.0 Consensus size: 24
128282 AAACGGAGAT
*
128292 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * * *
128316 AACA-ATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
*
128339 ATCAGAAATCAGAACAAAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * * *
128363 GTCATATATCAGAACATAATTCA
1 ATCAGAAATCAGAACAGAATTCA
128386 AGTCGGAAAT
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
23 19 0.34
24 37 0.66
ACGTcount: A:0.51, C:0.18, G:0.11, T:0.20
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:128397 original size:24 final size:24
Alignment explanation
Indices: 128340--128397 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
128330 AGAATCCAGA
*
128340 TCAGAAATCAGAACAAAATTCAGG
1 TCAGAAATCAGAACAAAATTCAAG
* * *
128364 TCATATATCAGAACATAATTCAAG
1 TCAGAAATCAGAACAAAATTCAAG
*
128388 TCGGAAATCA
1 TCAGAAATCA
128398 ATAAAATATT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (24 bp):
TCAGAAATCAGAACAAAATTCAAG
Found at i:129405 original size:26 final size:25
Alignment explanation
Indices: 129357--129415 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
129347 TGAGCTTGGT
*
129357 GGTATTCTTGGGTCATTTCTATTACAG
1 GGTATT-TTGGGTCATTTATATT-CAG
129384 GGTATTTT-GGTCATTTTATATTCAG
1 GGTATTTTGGGTCA-TTTATATTCAG
*
129409 TGTATTT
1 GGTATTT
129416 AATCCTTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 14 0.48
26 9 0.31
27 6 0.21
ACGTcount: A:0.19, C:0.10, G:0.20, T:0.51
Consensus pattern (25 bp):
GGTATTTTGGGTCATTTATATTCAG
Found at i:130109 original size:36 final size:36
Alignment explanation
Indices: 130062--130134 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
130052 GATAAATTAT
130062 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
* *
130098 AATCTACATATCGATGGTTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
130134 A
1 A
130135 TTCCAGAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (36 bp):
AATCTACATATCCATGGCTGATTCTTTTATCACTTA
Found at i:130758 original size:13 final size:13
Alignment explanation
Indices: 130740--130785 Score: 65
Period size: 13 Copynumber: 3.3 Consensus size: 13
130730 GTCGGTCAAC
130740 GGTCAACGGGTCG
1 GGTCAACGGGTCG
130753 GGTCAACGGTTGGTCG
1 GGTCAAC-G--GGTCG
130769 GGTCAACGGGTCG
1 GGTCAACGGGTCG
130782 GGTC
1 GGTC
130786 GGGTTGTGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 16 0.53
14 1 0.03
15 1 0.03
16 12 0.40
ACGTcount: A:0.13, C:0.22, G:0.46, T:0.20
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:130801 original size:29 final size:28
Alignment explanation
Indices: 130739--130803 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
130729 CGTCGGTCAA
*
130739 CGGTCAACGGGTCGGGTCAACGGTTGGTC
1 CGGTCAACGGGTCGGGTC-ACGGTTGGCC
* *
130768 GGGTCAACGGGTCGGGTC-GGGTTGTGACC
1 CGGTCAACGGGTCGGGTCACGGTTG-G-CC
130797 CGGTCAA
1 CGGTCAA
130804 AATAGTTCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
27 5 0.17
28 1 0.03
29 24 0.80
ACGTcount: A:0.14, C:0.23, G:0.43, T:0.20
Consensus pattern (28 bp):
CGGTCAACGGGTCGGGTCACGGTTGGCC
Found at i:134326 original size:146 final size:146
Alignment explanation
Indices: 133810--134560 Score: 1024
Period size: 146 Copynumber: 5.1 Consensus size: 146
133800 AGTTGATATA
* * * * *
133810 TCACTGAAAAGTTGTTGAAGATAATTGATAGGGCAATGAAAATTTGTTGGCATTTTCTGGCATGG
1 TCACTGAAAAGTTGCTGAAGATGATTGATGGGGCACTGAAAAGTTGTT-GCATTTTCTGGCATGG
* *
133875 TGCATTATTAATGGCATTTTTGAAGATTATTAATGGCCCATTTTGACA-TTTCGGGCAT-GTAGA
65 TGCATTATTAATGGCATTTTTGAAGATTATTAATGGCCCGTTTTGACATTTTCGGGCATGGT-GC
133938 ATTATTAGAGATGACATT
129 ATTATTAGAGATGACATT
* * * * *
133956 TCACTGAAAAGTTGTTGAAGATGATTGATGGGGCAATGAAAAATTGTTGACATATTCTGGTATGG
1 TCACTGAAAAGTTGCTGAAGATGATTGATGGGGCACTGAAAAGTTGTTG-CATTTTCTGGCATGG
* * *
134021 TGCATTATTAATTGCATTTTTGAAGATTATTAATAGCTCGTTTTGACATTTTCGGGCATGGTGCA
65 TGCATTATTAATGGCATTTTTGAAGATTATTAATGGCCCGTTTTGACATTTTCGGGCATGGTGCA
*
134086 TTATTAAAGATGACATT
130 TTATTAGAGATGACATT
* * *
134103 TCACTGAAAAGTTGCTGAAGATGATTAATGGTGCACTGAAAAGTTGTTGACATTTTCTGACATGG
1 TCACTGAAAAGTTGCTGAAGATGATTGATGGGGCACTGAAAAGTTGTTG-CATTTTCTGGCATGG
* *
134168 TGCATTATTAATGGCATTTTCTGAAGATTATTAATGGCCCG-TTTGATATATTCGGGCATGGTGC
65 TGCATTATTAATGGCATTTT-TGAAGATTATTAATGGCCCGTTTTGACATTTTCGGGCATGGTGC
* *
134232 ATTATTAGATATGAAATT
129 ATTATTAGAGATGACATT
* * * **
134250 TCACT-AAAAGTTGCTGAAGATGGTTGATTGGGCACTGAAAAGTTGTTAGCATTTTCTAGCATTA
1 TCACTGAAAAGTTGCTGAAGATGATTGATGGGGCACTGAAAAGTTGTT-GCATTTTCTGGCATGG
* *
134314 TGCATTATTAATGGCATTTTCTGAAGATTATTAATGGCCCGTTTTGACATTTTCGGGCATGTTGT
65 TGCATTATTAATGGCATTTT-TGAAGATTATTAATGGCCCGTTTTGACATTTTCGGGCATGGTGC
* *
134379 ATTATTACAGATGTCATT
129 ATTATTAGAGATGACATT
* * * * *
134397 TCACTGAAAAGTTACTGAAGATTATTGATGGGGCACTGAAAAGTTACTGGCATTTTCTGGCATGT
1 TCACTGAAAAGTTGCTGAAGATGATTGATGGGGCACTGAAAAGTT-GTTGCATTTTCTGGCATGG
*
134462 TGCATTATTAATGGCATTTTTTGAAGATTATTAATGGCCCGTTTTGACATTTTTGGGCATGGTGC
65 TGCATTATTAATGGCA-TTTTTGAAGATTATTAATGGCCCGTTTTGACATTTTCGGGCATGGTGC
134527 ATTATTAGAGATGACATT
129 ATTATTAGAGATGACATT
* * *
134545 TTACTAAAAAGCTGCT
1 TCACTGAAAAGTTGCT
134561 AAAGCTTATT
Statistics
Matches: 535, Mismatches: 61, Indels: 16
0.87 0.10 0.03
Matches are distributed among these distances:
145 1 0.00
146 192 0.36
147 184 0.34
148 153 0.29
149 5 0.01
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.38
Consensus pattern (146 bp):
TCACTGAAAAGTTGCTGAAGATGATTGATGGGGCACTGAAAAGTTGTTGCATTTTCTGGCATGGT
GCATTATTAATGGCATTTTTGAAGATTATTAATGGCCCGTTTTGACATTTTCGGGCATGGTGCAT
TATTAGAGATGACATT
Found at i:134399 original size:294 final size:290
Alignment explanation
Indices: 133810--134553 Score: 1033
Period size: 294 Copynumber: 2.5 Consensus size: 290
133800 AGTTGATATA
* * *
133810 TCACTGAAAAGTTGTTGAAGATAATTGATAGGGCAATGAAAATTTGTTGGCATTTTCTGGCATGG
1 TCACTGAAAAGTTGCTGAAGATAATTGAT-GGGCACTGAAAAGTTGTTGGCATTTTCTGGCATGG
* *
133875 TGCATTATTAATGGCATTTTTGAAGATTATTAATGGCCCATTTTGACATTTCGGGCAT-GTAGAA
65 TGCATTATTAATGGCATTTTTGAAGATTATTAATGGCCC-GTTTGACATTTCGGGCATGGT-GCA
*
133939 TTATTAGAGATGACATTTCACTGAAAAGTTGTTGAAGATGATTGATGGGGCAATGAAAAATTGTT
128 TTATTAGAGATGACATTTCACT-AAAAGTTGCTGAAGATGATTGATGGGGCAATGAAAAATTGTT
* * * * *
134004 GACATATTCTGGTATGGTGCATTATTAATTGCATTTTTGAAGATTATTAATAGCTCGTTTTGACA
192 GACATATTCTAGCATGATGCATTATTAATGGCATTTTTGAAGATTATTAATAGCCCGTTTTGACA
134069 TTTTCGGGCATGGTGCATTATTAAAGATGACATT
257 TTTTCGGGCATGGTGCATTATTAAAGATGACATT
* * * *
134103 TCACTGAAAAGTTGCTGAAGATGATTAATGGTGCACTGAAAAGTTGTTGACATTTTCTGACATGG
1 TCACTGAAAAGTTGCTGAAGATAATTGATGG-GCACTGAAAAGTTGTTGGCATTTTCTGGCATGG
*
134168 TGCATTATTAATGGCATTTTCTGAAGATTATTAATGGCCCGTTTGATATATTCGGGCATGGTGCA
65 TGCATTATTAATGGCATTTT-TGAAGATTATTAATGGCCCGTTTGACAT-TTCGGGCATGGTGCA
* * * * * *
134233 TTATTAGATATGAAATTTCACTAAAAGTTGCTGAAGATGGTTGATTGGGCACTGAAAAGTTGTT-
128 TTATTAGAGATGACATTTCACTAAAAGTTGCTGAAGATGATTGATGGGGCAATGAAAAATTGTTG
* * *
134297 AGCATTTTCTAGCATTATGCATTATTAATGGCATTTTCTGAAGATTATTAATGGCCCGTTTTGAC
193 A-CATATTCTAGCATGATGCATTATTAATGGCATTTT-TGAAGATTATTAATAGCCCGTTTTGAC
* * * *
134362 ATTTTCGGGCATGTTGTATTATTACAGATGTCATT
256 ATTTTCGGGCATGGTGCATTATTAAAGATGACATT
* * ** *
134397 TCACTGAAAAGTTACTGAAGATTATTGATGGGGCACTGAAAAGTTACTGGCATTTTCTGGCATGT
1 TCACTGAAAAGTTGCTGAAGATAATTGAT-GGGCACTGAAAAGTTGTTGGCATTTTCTGGCATGG
*
134462 TGCATTATTAATGGCATTTTTTGAAGATTATTAATGGCCCGTTTTGACATTTTTGGGCATGGTGC
65 TGCATTATTAATGGCA-TTTTTGAAGATTATTAATGGCCCG-TTTGACA-TTTCGGGCATGGTGC
*
134527 ATTATTAGAGATGACATTTTACTAAAA
127 ATTATTAGAGATGACATTTCACTAAAA
134554 AGCTGCTAAA
Statistics
Matches: 399, Mismatches: 42, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
292 3 0.01
293 148 0.37
294 196 0.49
295 51 0.13
296 1 0.00
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.38
Consensus pattern (290 bp):
TCACTGAAAAGTTGCTGAAGATAATTGATGGGCACTGAAAAGTTGTTGGCATTTTCTGGCATGGT
GCATTATTAATGGCATTTTTGAAGATTATTAATGGCCCGTTTGACATTTCGGGCATGGTGCATTA
TTAGAGATGACATTTCACTAAAAGTTGCTGAAGATGATTGATGGGGCAATGAAAAATTGTTGACA
TATTCTAGCATGATGCATTATTAATGGCATTTTTGAAGATTATTAATAGCCCGTTTTGACATTTT
CGGGCATGGTGCATTATTAAAGATGACATT
Found at i:134506 original size:23 final size:23
Alignment explanation
Indices: 134465--134508 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
134455 GGCATGTTGC
**
134465 ATTATTAATGGCATTTTTTGAAG
1 ATTATTAATGGCACGTTTTGAAG
*
134488 ATTATTAATGGCCCGTTTTGA
1 ATTATTAATGGCACGTTTTGA
134509 CATTTTTGGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.09, G:0.18, T:0.45
Consensus pattern (23 bp):
ATTATTAATGGCACGTTTTGAAG
Found at i:136397 original size:23 final size:23
Alignment explanation
Indices: 136371--136448 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
136361 CACCACAGCT
136371 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
136394 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* *
136417 CATAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
136440 TATAATAAT
1 CAT-ATAAT
136449 GTCCATAAAG
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 43 0.91
24 4 0.09
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:136626 original size:103 final size:103
Alignment explanation
Indices: 136458--136672 Score: 403
Period size: 103 Copynumber: 2.1 Consensus size: 103
136448 TGTCCATAAA
* *
136458 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
136523 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
*
136561 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
136626 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
136664 GACCACATA
1 GACCACATA
136673 GACCCTCGAC
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
Found at i:141438 original size:23 final size:23
Alignment explanation
Indices: 141412--141489 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
141402 CACCACAGCT
141412 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* * * *
141435 CATATAATTACACTGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* * *
141458 TATAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
141481 TATAATAAT
1 CAT-ATAAT
141490 GTCCATAAGG
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 39 0.91
24 4 0.09
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.27
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:141672 original size:103 final size:97
Alignment explanation
Indices: 141499--141707 Score: 328
Period size: 103 Copynumber: 2.1 Consensus size: 97
141489 TGTCCATAAG
*
141499 GACCACATATCATTCTTTAAGAATCATATACTAGGGATCAAGTATGTGTCTCACCAGACTTCACA
1 GACCACATATCATTCCTTAAGAATCATATACTAGGGATCAAGTATGTGTCTCACCAGACTTCACA
*
141564 CATGTTCCAAACAATACATATATGTTCCGAAA
66 CATGTTCCAAACAATACATATATGTCCCGAAA
141596 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATAC-TA-G----GGATCAAGTATGTGTCTCACCAGAC
* *
141661 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
60 TTCACACATGTTCCAAACAATACATATATGTCCCGAAA
141699 GACCACATA
1 GACCACATA
141708 GACACTCGAC
Statistics
Matches: 102, Mismatches: 4, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
97 30 0.29
98 2 0.02
99 1 0.01
103 69 0.68
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (97 bp):
GACCACATATCATTCCTTAAGAATCATATACTAGGGATCAAGTATGTGTCTCACCAGACTTCACA
CATGTTCCAAACAATACATATATGTCCCGAAA
Found at i:141856 original size:24 final size:24
Alignment explanation
Indices: 141820--141872 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
141810 TGAAATCCTT
*
141820 TCACATAGCTCAT-TGTCATATAAA
1 TCACATAGCTCATAT-ACATATAAA
**
141844 TCACATATTTCATATACATATAAA
1 TCACATAGCTCATATACATATAAA
141868 -CACAT
1 TCACAT
141873 GGTTTACCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 5 0.20
24 19 0.76
25 1 0.04
ACGTcount: A:0.42, C:0.21, G:0.04, T:0.34
Consensus pattern (24 bp):
TCACATAGCTCATATACATATAAA
Found at i:147622 original size:3 final size:3
Alignment explanation
Indices: 147614--147667 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
147604 TGAATAACTG
147614 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
147662 ATA ATA
1 ATA ATA
147668 TTCGGAACCA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:148105 original size:13 final size:13
Alignment explanation
Indices: 148087--148114 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
148077 TTTAGTATCG
148087 TACGTATTAATAT
1 TACGTATTAATAT
148100 TACGTATTAATAT
1 TACGTATTAATAT
148113 TA
1 TA
148115 AGAATATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (13 bp):
TACGTATTAATAT
Found at i:149911 original size:21 final size:21
Alignment explanation
Indices: 149887--149927 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
149877 GATTATGAAT
149887 ATGAAGAA-ATATAATATTAAA
1 ATGAA-AATATATAATATTAAA
*
149908 ATGAAAATATATGATATTAA
1 ATGAAAATATATAATATTAA
149928 CACGAAGAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.32
Consensus pattern (21 bp):
ATGAAAATATATAATATTAAA
Found at i:151290 original size:144 final size:144
Alignment explanation
Indices: 151028--151301 Score: 494
Period size: 144 Copynumber: 1.9 Consensus size: 144
151018 ATGATCCTTC
*
151028 ATTTAGGTTTGTTTTACTTTTAATAATTATTGAGTTAAGGGGAAAATAGAACTAAATTATTGGGC
1 ATTTAGGTTTGTTTTACTTTTAATAATTATCGAGTTAAGGGGAAAATAGAACTAAATTATTGGGC
* *
151093 AAAAAGGTCAACTTTGAACGAGTCTTTATATACCAACCTTTGGATTGACATATGATCCTTCATTT
66 AAAAAGGTCAACTTTGAACGAGTCTTTATATAACAACCTTTGGATTGAAATATGATCCTTCATTT
151158 AGGTTAAAATGTCT
131 AGGTTAAAATGTCT
* *
151172 ATTTAGGTTTGTTTTGCTTTTAATAATTATCGAGTTAAGGGGAAAATATAACTAAATTATTGGGC
1 ATTTAGGTTTGTTTTACTTTTAATAATTATCGAGTTAAGGGGAAAATAGAACTAAATTATTGGGC
*
151237 AAAAAGGTCAACTTTGAGCGAGTCTTTATATAACAACCTTTGGATTGAAATATGATCCTTCATTT
66 AAAAAGGTCAACTTTGAACGAGTCTTTATATAACAACCTTTGGATTGAAATATGATCCTTCATTT
151302 TTAATAGTAT
Statistics
Matches: 124, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
144 124 1.00
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (144 bp):
ATTTAGGTTTGTTTTACTTTTAATAATTATCGAGTTAAGGGGAAAATAGAACTAAATTATTGGGC
AAAAAGGTCAACTTTGAACGAGTCTTTATATAACAACCTTTGGATTGAAATATGATCCTTCATTT
AGGTTAAAATGTCT
Found at i:157102 original size:17 final size:18
Alignment explanation
Indices: 157063--157108 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
157053 TATTTCTAAG
157063 GGAATTAGAATCTGTGAA
1 GGAATTAGAATCTGTGAA
*
157081 GGAATTAGAATCTGT-CA
1 GGAATTAGAATCTGTGAA
*
157098 GGAATTTGAAT
1 GGAATTAGAAT
157109 TTGAATGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (18 bp):
GGAATTAGAATCTGTGAA
Found at i:157627 original size:18 final size:18
Alignment explanation
Indices: 157586--157621 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
157576 AGTGCCTTAA
*
157586 AAACCCTAAACTCGACCC
1 AAACCCTAAACCCGACCC
157604 AAACCCTAAACCCGACCC
1 AAACCCTAAACCCGACCC
157622 CGACCCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.47, G:0.06, T:0.08
Consensus pattern (18 bp):
AAACCCTAAACCCGACCC
Found at i:159396 original size:17 final size:17
Alignment explanation
Indices: 159374--159408 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
159364 CCAATATCCC
159374 AAGCGGGTTAATTATTT
1 AAGCGGGTTAATTATTT
159391 AAGCGGGTTAATTATTT
1 AAGCGGGTTAATTATTT
159408 A
1 A
159409 GGGTATTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.06, G:0.23, T:0.40
Consensus pattern (17 bp):
AAGCGGGTTAATTATTT
Found at i:159611 original size:14 final size:14
Alignment explanation
Indices: 159552--159611 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
159542 TGACGAGTTC
*
159552 AATTAAAAATAATA
1 AATTAAAAAAAATA
*
159566 ATTATAAAAATAAAATA
1 A--ATTAAAA-AAAATA
**
159583 AATTAAAAAGTATA
1 AATTAAAAAAAATA
159597 AATTAAAAAAAATA
1 AATTAAAAAAAATA
159611 A
1 A
159612 GTAGAACTCG
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
14 18 0.50
15 6 0.17
16 6 0.17
17 6 0.17
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.27
Consensus pattern (14 bp):
AATTAAAAAAAATA
Found at i:160937 original size:20 final size:20
Alignment explanation
Indices: 160912--160950 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
160902 AAAATTTTAA
160912 AAATAAAAAATATTATAAAC
1 AAATAAAAAATATTATAAAC
*
160932 AAATAAAAAATATTTTAAA
1 AAATAAAAAATATTATAAA
160951 TTTATGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (20 bp):
AAATAAAAAATATTATAAAC
Found at i:162210 original size:18 final size:18
Alignment explanation
Indices: 162187--162232 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
162177 CAACATTCCC
*
162187 GGTAATCTTATTCCCGCA
1 GGTAATCTTATTCCCACA
* *
162205 GGTAATCATATTCCCACT
1 GGTAATCTTATTCCCACA
162223 GGTAATCTTA
1 GGTAATCTTA
162233 CATTATGTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (18 bp):
GGTAATCTTATTCCCACA
Found at i:165849 original size:30 final size:29
Alignment explanation
Indices: 165794--165850 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
165784 CTCCCTGAGC
*
165794 AATTAGGACCCCTATTTTTTCATCTTTAT
1 AATTAGGACCCCTATTTTTTAATCTTTAT
*
165823 AATTAGG-CTCCTAATTTTTTAAATCTTT
1 AATTAGGACCCCT-ATTTTTT-AATCTTT
165851 TTTTTACCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.17
29 14 0.58
30 6 0.25
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49
Consensus pattern (29 bp):
AATTAGGACCCCTATTTTTTAATCTTTAT
Found at i:165905 original size:43 final size:42
Alignment explanation
Indices: 165817--166280 Score: 355
Period size: 44 Copynumber: 10.6 Consensus size: 42
165807 ATTTTTTCAT
* **
165817 CTTTATAATT-AGGCTCCTAATTTTTTAAATCT-TTTTTTTAC
1 CTTTATAATTGAGGC-CCTAATTTTTTCAATCTCACTTTTTAC
* * * *
165858 CTTTACAATTGAGGTCCTAATTTAATTCAATCTCACTTTTTAT
1 CTTTATAATTGAGGCCCTAATTT-TTTCAATCTCACTTTTTAC
* * **
165901 CTTTATAATTGAAGTCTCTAATTTTTTCAATCTCTTTTTTTAC
1 CTTTATAATTG-AGGCCCTAATTTTTTCAATCTCACTTTTTAC
* * *
165944 CTTTATAATTGAGCCCCTAATTTTTT-AATCTCATTTTTTAA
1 CTTTATAATTGAGGCCCTAATTTTTTCAATCTCACTTTTTAC
* * * *
165985 CTTTATAATTAAGGCCCTTAAGTTTCAATCTCACTTTCTACCTTTTTCTAC
1 CTTTATAATTGAGGCCC-TAA-TTT---TTTCAATCTC-A-C-TTTT-TAC
* * * *
166036 CTTTACAATTGATGCCCCTAATTTTTT-AATCCCACTTTTTTAA
1 CTTTATAATTGA-GGCCCTAATTTTTTCAATCTCAC-TTTTTAC
* *
166079 CTTTATAATTGAGGCTCTTAAGTTTTTTCAATCTCACTTTCTAC
1 CTTTATAATTGAGGC-CCTAA-TTTTTTCAATCTCACTTTTTAC
* * * *
166123 TTTTATAATTGAGACCCCTAAGTTTTTTTAATCTCAATTTTTAC
1 CTTTATAATTGAG-GCCCTAA-TTTTTTCAATCTCACTTTTTAC
* *
166167 CTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCA-ATTATAC
1 CTTTATAATTGAGG-CCCTAA-TTTTTTCAATCTCACTTTTTAC
* * *
166210 CTTTACAATTGAGGCCCCTGATTTTTTTTCAATCTC-CATTTCTAC
1 CTTTATAATTGAGG-CCCT-A-ATTTTTTCAATCTCAC-TTTTTAC
* *
166255 CTTTATAATTAAGGCTCTAATTTTTT
1 CTTTATAATTGAGGCCCTAATTTTTT
166281 TTCCAATTTC
Statistics
Matches: 340, Mismatches: 59, Indels: 47
0.76 0.13 0.11
Matches are distributed among these distances:
41 45 0.13
42 34 0.10
43 86 0.25
44 111 0.33
45 26 0.08
46 5 0.01
47 6 0.02
48 1 0.00
50 7 0.02
51 15 0.04
52 4 0.01
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.49
Consensus pattern (42 bp):
CTTTATAATTGAGGCCCTAATTTTTTCAATCTCACTTTTTAC
Found at i:166099 original size:94 final size:92
Alignment explanation
Indices: 165934--166126 Score: 289
Period size: 94 Copynumber: 2.1 Consensus size: 92
165924 TTTTCAATCT
* * *
165934 CTTTTTTTACCTTTATAATTGAGCCCCTAATTTTTTAATCTCATTTTTTAACTTTATAATTAAGG
1 CTTTTTCTACCTTTACAATTGAGCCCCTAATTTTTTAATCCCATTTTTTAACTTTATAATTAAGG
165999 CCCTTAAG-TTTCAATCTCACTTTCTA
66 CCCTTAAGTTTTCAATCTCACTTTCTA
*
166025 CCTTTTTCTACCTTTACAATTGATGCCCCTAATTTTTTAATCCCACTTTTTTAACTTTATAATTG
1 -CTTTTTCTACCTTTACAATTGA-GCCCCTAATTTTTTAATCCCA-TTTTTTAACTTTATAATTA
*
166090 AGGCTCTTAAGTTTTTTCAATCTCACTTTCTA
63 AGGCCCTTAAG--TTTTCAATCTCACTTTCTA
166122 CTTTT
1 CTTTT
166127 ATAATTGAGA
Statistics
Matches: 91, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
92 20 0.22
93 20 0.22
94 28 0.31
96 5 0.05
97 18 0.20
ACGTcount: A:0.23, C:0.21, G:0.06, T:0.50
Consensus pattern (92 bp):
CTTTTTCTACCTTTACAATTGAGCCCCTAATTTTTTAATCCCATTTTTTAACTTTATAATTAAGG
CCCTTAAGTTTTCAATCTCACTTTCTA
Found at i:166924 original size:2 final size:2
Alignment explanation
Indices: 166917--166959 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
166907 TAAGTAATTT
166917 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
166959 T
1 T
166960 TTGGACAGCA
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:167115 original size:18 final size:19
Alignment explanation
Indices: 167092--167129 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
167082 CATTAAAAAT
*
167092 ATAAAAG-AACAATAATAA
1 ATAAAAGAAAAAATAATAA
167110 ATAAAAGAAAAAATAATAA
1 ATAAAAGAAAAAATAATAA
167129 A
1 A
167130 ATAATTGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (19 bp):
ATAAAAGAAAAAATAATAA
Found at i:168784 original size:88 final size:88
Alignment explanation
Indices: 168635--168807 Score: 337
Period size: 88 Copynumber: 2.0 Consensus size: 88
168625 TTCGTCTATG
168635 ATATATACCTTACATGAACAGGTAATATACGATACATCTAAAGTCTAATGCCCAAATATGTAATT
1 ATATATACCTTACATGAACAGGTAATATACGATACATCTAAAGTCTAATGCCCAAATATGTAATT
*
168700 TGCATAGGGTGGTATGTGTGTAT
66 TGCATAGGGTGATATGTGTGTAT
168723 ATATATACCTTACATGAACAGGTAATATACGATACATCTAAAGTCTAATGCCCAAATATGTAATT
1 ATATATACCTTACATGAACAGGTAATATACGATACATCTAAAGTCTAATGCCCAAATATGTAATT
168788 TGCATAGGGTGATATGTGTG
66 TGCATAGGGTGATATGTGTG
168808 CGTGTGTATA
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 84 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (88 bp):
ATATATACCTTACATGAACAGGTAATATACGATACATCTAAAGTCTAATGCCCAAATATGTAATT
TGCATAGGGTGATATGTGTGTAT
Found at i:168920 original size:3 final size:3
Alignment explanation
Indices: 168908--168937 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
168898 AAGTACAATG
168908 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
168938 GTTATATGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:171674 original size:10 final size:10
Alignment explanation
Indices: 171659--171684 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
171649 CTGTGACCGT
171659 CACCGCCGGC
1 CACCGCCGGC
171669 CACCGCCGGC
1 CACCGCCGGC
171679 CACCGC
1 CACCGC
171685 ATCTGGTGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.62, G:0.27, T:0.00
Consensus pattern (10 bp):
CACCGCCGGC
Found at i:172452 original size:3 final size:3
Alignment explanation
Indices: 172444--172519 Score: 134
Period size: 3 Copynumber: 25.3 Consensus size: 3
172434 TTAATATATT
*
172444 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
172492 TAA TGA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
172520 GATATGGGTA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:173086 original size:113 final size:113
Alignment explanation
Indices: 172842--173492 Score: 1142
Period size: 113 Copynumber: 5.8 Consensus size: 113
172832 AGAATTATGC
* * * *
172842 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
172907 TATGAAC-TTCTCCGGAAAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
172954 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
173019 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
173067 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
173132 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
173180 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
173245 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
* * *
173293 AAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
173358 TATGAACTTTCTCTGGAAAAAATAATCCATCAATTTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAA-ATGATGAATTCAGGT
173407 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
173472 TATGAACCTTCTCTGGAAAAG
66 TATGAACTTTCTCTGGAAAAG
173493 CTAATCTTTC
Statistics
Matches: 517, Mismatches: 20, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
112 68 0.13
113 355 0.69
114 94 0.18
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
Found at i:174442 original size:83 final size:83
Alignment explanation
Indices: 174303--174881 Score: 1011
Period size: 83 Copynumber: 7.0 Consensus size: 83
174293 TCTACTATGA
* * *
174303 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCAAACCATATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
174368 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
* * *
174386 GCAAATTCATCTTCAAAATTCAATGATTGGTCCTGCCAAACCAGATCAAATAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
174451 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
* *
174469 GCAAATTCATCTTCAAAATTTAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
*
174534 TTCCAGAAGATGCTATCG
66 TTCCAGAAGATGCTATTG
*
174552 ACAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
174617 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
174635 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAAAGAACA
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACA
174699 CTTCCAGAAGATGCTATTG
65 CTTCCAGAAGATGCTATTG
174718 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAAAGAACA
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACA
174782 CTTCCAGAAGATGCTATTG
65 CTTCCAGAAGATGCTATTG
*
174801 GCAAATTCATCTTCTAAATTCAATGATTGGTTATGTCC-AACCAGATCAGATAACTCAAAGAACA
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACA
174865 CTTCCAGAAGATGCTAT
65 CTTCCAGAAGATGCTAT
174882 GGAGCACATT
Statistics
Matches: 480, Mismatches: 15, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
83 478 1.00
84 2 0.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.28
Consensus pattern (83 bp):
GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
TTCCAGAAGATGCTATTG
Found at i:175951 original size:7 final size:7
Alignment explanation
Indices: 175939--175971 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
175929 TTTTCTTCTT
*
175939 TTTTTTC
1 TTTTTTA
175946 TTTTTTA
1 TTTTTTA
175953 TTTTTTA
1 TTTTTTA
175960 -TTTTTA
1 TTTTTTA
175966 TTTTTT
1 TTTTTT
175972 TTTCAACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.09, C:0.03, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:175951 original size:9 final size:9
Alignment explanation
Indices: 175924--175973 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
175914 CCTTGACCCA
175924 TTTCTTTTT
1 TTTCTTTTT
*
175933 CTTCTTTTT
1 TTTCTTTTT
175942 TTTCTTTTT
1 TTTCTTTTT
*
175951 TATTTTTTATT
1 T-TTCTTT-TT
*
175962 TTTATTTTT
1 TTTCTTTTT
175971 TTT
1 TTT
175974 TCAACTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
9 22 0.63
10 10 0.29
11 3 0.09
ACGTcount: A:0.06, C:0.08, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:175956 original size:13 final size:12
Alignment explanation
Indices: 175940--175974 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
175930 TTTCTTCTTT
175940 TTTTTCTTTTTTA
1 TTTTT-TTTTTTA
175953 TTTTTTATTTTTA
1 TTTTTT-TTTTTA
175966 TTTTTTTTT
1 TTTTTTTTT
175975 CAACTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.09, C:0.03, G:0.00, T:0.89
Consensus pattern (12 bp):
TTTTTTTTTTTA
Found at i:187608 original size:15 final size:15
Alignment explanation
Indices: 187567--187608 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
187557 CCTCGGTGAG
*
187567 TTTCTTTTCTTCCTT
1 TTTCTTTTCTTTCTT
*
187582 TTTCTTTCCTTTC-T
1 TTTCTTTTCTTTCTT
187596 TTTCTGTTTCTTT
1 TTTCT-TTTCTTT
187609 GCTGAGTGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.74
Consensus pattern (15 bp):
TTTCTTTTCTTTCTT
Found at i:188168 original size:3 final size:3
Alignment explanation
Indices: 188160--188241 Score: 146
Period size: 3 Copynumber: 27.3 Consensus size: 3
188150 TTAATATATT
*
188160 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
188208 TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
188242 GATATGGGTA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:194516 original size:42 final size:42
Alignment explanation
Indices: 194462--194552 Score: 155
Period size: 42 Copynumber: 2.2 Consensus size: 42
194452 AAAATGAAAC
* *
194462 TTTAGCGGCGTTTTTTCAACAAACGCCGCAATAGGGTGGTAA
1 TTTAGCGACGTTTTTTCAACAAACGCCACAATAGGGTGGTAA
*
194504 TTTAGCGACGTTTTTTCAACAAACGCCATAATAGGGTGGTAA
1 TTTAGCGACGTTTTTTCAACAAACGCCACAATAGGGTGGTAA
194546 TTTAGCG
1 TTTAGCG
194553 GCGCTTATAG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (42 bp):
TTTAGCGACGTTTTTTCAACAAACGCCACAATAGGGTGGTAA
Found at i:194570 original size:42 final size:42
Alignment explanation
Indices: 194478--194563 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 42
194468 GGCGTTTTTT
* * **
194478 CAACAAACGCCGCAATAGGGTGGTAATTTAGCGACGTTTTTT
1 CAACAAACGCCACAATAGGGTGGTAATTTAGCGACGTTATAG
* *
194520 CAACAAACGCCATAATAGGGTGGTAATTTAGCGGCGCTTATAG
1 CAACAAACGCCACAATAGGGTGGTAATTTAGCGACG-TTATAG
194563 C
1 C
194564 TCAAACGTCG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 33 0.89
43 4 0.11
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (42 bp):
CAACAAACGCCACAATAGGGTGGTAATTTAGCGACGTTATAG
Found at i:196806 original size:30 final size:30
Alignment explanation
Indices: 196750--196808 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
196740 GAAGAACCAG
* *
196750 CTGAAAACCGGGAAAATCGGGGTGAACCGA
1 CTGAAAACCGGCAAAACCGGGGTGAACCGA
**
196780 CTGAAAACCGGCAAAACCGGTTTGAACCG
1 CTGAAAACCGGCAAAACCGGGGTGAACCG
196809 CCGGTTCATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.36, C:0.24, G:0.29, T:0.12
Consensus pattern (30 bp):
CTGAAAACCGGCAAAACCGGGGTGAACCGA
Found at i:203951 original size:21 final size:22
Alignment explanation
Indices: 203925--204036 Score: 108
Period size: 21 Copynumber: 5.3 Consensus size: 22
203915 AGCGGAAAAT
*
203925 GAAGCAAG-GGAAGCAGAGAGA
1 GAAGCAAGCGGAAGCACAGAGA
*
203946 GCAGC-AGCGGAAGCACAGAGA
1 GAAGCAAGCGGAAGCACAGAGA
* * *
203967 GAAGC-AGTGGCAGCACACAGA
1 GAAGCAAGCGGAAGCACAGAGA
* *
203988 GAGGC-AGCGGTAGCACAGAGA
1 GAAGCAAGCGGAAGCACAGAGA
* *
204009 GAAGC-AGCTGCAGCACAGAGA
1 GAAGCAAGCGGAAGCACAGAGA
204030 GAAGCAA
1 GAAGCAA
204037 TATATCAACA
Statistics
Matches: 76, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
20 2 0.03
21 73 0.96
22 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.38, T:0.03
Consensus pattern (22 bp):
GAAGCAAGCGGAAGCACAGAGA
Found at i:203995 original size:42 final size:42
Alignment explanation
Indices: 203949--204031 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
203939 AGAGAGAGCA
203949 GCAGCGGAAGCACAGAGAGAAGCAG-TGGCAGCACACAGAGAG
1 GCAGCGGAAGCACAGAGAGAAGCAGCT-GCAGCACACAGAGAG
* *
203991 GCAGCGGTAGCACAGAGAGAAGCAGCTGCAGCACAGAGAGA
1 GCAGCGGAAGCACAGAGAGAAGCAGCTGCAGCACACAGAGA
204032 AGCAATATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 37 0.97
43 1 0.03
ACGTcount: A:0.37, C:0.22, G:0.37, T:0.04
Consensus pattern (42 bp):
GCAGCGGAAGCACAGAGAGAAGCAGCTGCAGCACACAGAGAG
Found at i:204476 original size:43 final size:42
Alignment explanation
Indices: 204372--204554 Score: 154
Period size: 43 Copynumber: 4.3 Consensus size: 42
204362 CATACATTTA
* ** *
204372 GCGGCGTTTGTGATAAAAACGCCGCCAAATCTCAAGA-CATATT
1 GCGGCGTTTGTGA-AAAAACGCCGCTAAAAATCAACATC-TATT
* * * * * *
204415 ACGACATTT-TCGATAAAAACGCTGCTAAATATCAACATCTTTT
1 GCGGCGTTTGT-GA-AAAAACGCCGCTAAAAATCAACATCTATT
* * * *
204458 GTGGCGTTTGTGGGAAAAACGCCGGTAAAAATCAACATCTACT
1 GCGGCGTTTGT-GAAAAAACGCCGCTAAAAATCAACATCTATT
* *
204501 GCGACGTTTGTGAATAAAACGCCGCTAAACATCAACATCTATT
1 GCGGCGTTTGTGAA-AAAACGCCGCTAAAAATCAACATCTATT
204544 GCGGCGTTTGT
1 GCGGCGTTTGT
204555 TTGCCAAATG
Statistics
Matches: 110, Mismatches: 26, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
42 3 0.03
43 104 0.95
44 3 0.03
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (42 bp):
GCGGCGTTTGTGAAAAAACGCCGCTAAAAATCAACATCTATT
Found at i:204568 original size:43 final size:43
Alignment explanation
Indices: 204430--204641 Score: 167
Period size: 43 Copynumber: 4.9 Consensus size: 43
204420 ATTTTCGATA
* * * ** *
204430 AAAACGCTGCTAAATATCAACATCTTTTGTGGCGTTTGTGGGA
1 AAAACGCCGCTAAATATCAACATCTATTGCGGCGTTTGTTTGC
* * * * ****
204473 AAAACGCCGGTAAAAATCAACATCTACTGCGACGTTTGTGAAT
1 AAAACGCCGCTAAATATCAACATCTATTGCGGCGTTTGTTTGC
*
204516 AAAACGCCGCTAAACATCAACATCTATTGCGGCGTTTGTTTGC
1 AAAACGCCGCTAAATATCAACATCTATTGCGGCGTTTGTTTGC
* * * * *
204559 CAAATGCCGCTAAATATCAATC-CCTATTACGGCATTT-TTCTGC
1 AAAACGCCGCTAAATATCAA-CATCTATTGCGGCGTTTGTT-TGC
* * * * *
204602 CAAGCGCCGCTAAATATCAATACCTTTTGCGGCGTTTGTT
1 AAAACGCCGCTAAATATCAACATCTATTGCGGCGTTTGTT
204642 ATGTTGTCAC
Statistics
Matches: 135, Mismatches: 30, Indels: 7
0.78 0.17 0.04
Matches are distributed among these distances:
42 2 0.01
43 130 0.96
44 3 0.02
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (43 bp):
AAAACGCCGCTAAATATCAACATCTATTGCGGCGTTTGTTTGC
Found at i:219585 original size:27 final size:28
Alignment explanation
Indices: 219549--219604 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
219539 GAAGAATTAC
**
219549 TTCCACTTCTTGTAGCGTTTCCCAAACT
1 TTCCACTTCTTCCAGCGTTTCCCAAACT
219577 TTCC-CTTCTTCCAGCGTTTCCCAAACT
1 TTCCACTTCTTCCAGCGTTTCCCAAACT
219604 T
1 T
219605 CCCGTGCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.16, C:0.36, G:0.09, T:0.39
Consensus pattern (28 bp):
TTCCACTTCTTCCAGCGTTTCCCAAACT
Found at i:222351 original size:378 final size:376
Alignment explanation
Indices: 221674--222412 Score: 877
Period size: 378 Copynumber: 2.0 Consensus size: 376
221664 TATTAGATAG
* * ** * *
221674 CTCAGCAGGATTAGATTTGTGGCCTTGTTGAAATGCGTTATGTATATCCTCTTGATATCTCACCT
1 CTCAGCAGGATTAGATTTGTGGCCTTGTTGAAAAGCATTATGTATATCCTCCAGAGATCTCACAT
* * *
221739 CGACAACAGGTAATACTGAATTCGTATCTGTATGACCCTGCTGATTCTCAATCATACTTGGAAGA
66 CGACAACAGGTAATACTGAATTCGTATCTGCATGACCCTGCTAATTCTCAATCATACTAGGAAGA
*
221804 ATTACTTCCTCCACATCTACCCCTTCATGAAGTTGCTTAAAAACCAAATCAATGCCTTCAACTGA
131 ATTACTTCCTCAACATCTACCCCTTCATGAAGTTGCTTAAAAACCAAATCAATGCCTTCAACTGA
* * * * *
221869 TTTTGCTTCAAGAACAGGTAGTGCCGCCTTGGTCTCCATCTCTATTTCTTCTGTATCTTCATATC
196 TCTTGCTTCAAGAACAGGCAGTGCCACCTTGGTCTCCATCTCTATTTCTTCTGTATCATCAAATC
* * * * *
221934 CATCTTTCAGTTCACCAGCAGTATTCTCGTTTGTTTCTTGAATACCTGAGACGGAATTACTACCA
261 CATCTTTCAGTTCACCAGCAGTATTCACGTATGTTTCTTGAATACCAGAGACGCAATGACTACCA
221999 TCAATCTGCTTC-GTAGAAACCACATCATGATCTGCTCCTGTTGAATGTAGCAA
326 TCAATCT-CTTCAGTAGAAACCACATCATG-T-TGCTCCTGTTGAATGTAGCAA
* * **
222052 CTCAGCTGGATTAGATTTG-GTGCCTTGTTGAAAAGCATTATGTATGTCCTCCAGAGATCTTGCA
1 CTCAGCAGGATTAGATTTGTG-GCCTTGTTGAAAAGCATTATGTATATCCTCCAGAGATCTCACA
* * *
222116 TCGACAACAGGTAA-ATCTGAATTGGTATCTGCATGACCCTGGTAATTCTCAATCATGCTAGGAA
65 TCGACAACAGGTAATA-CTGAATTCGTATCTGCATGACCCTGCTAATTCTCAATCATACTAGGAA
* * * * *
222180 GAATTATTTCCTCAACATCTACTCCTTCATGGAGTTGCTTAAAAGCCAAATCAATGTCTTTCAA-
129 GAATTACTTCCTCAACATCTACCCCTTCATGAAGTTGCTTAAAAACCAAATCAATG-CCTTCAAC
** ** *
222244 TGATCTTGCTTCAAGAACAGGCAGCT-CCATGTTGGTCTCTGTCT-TCATTTCTTC-GATTTCAT
193 TGATCTTGCTTCAAGAACAGGCAG-TGCCACCTTGGTCTCCATCTCT-ATTTCTTCTG-TATCAT
* * * ** * *
222306 CAAAGT-CATTTTTCGGTTCGCTGGCAGTGTTCA-GACTAT-TTTCTTGAATACCAGAGACGCCA
255 CAAA-TCCATCTTTCAGTTCACCAGCAGTATTCACG--TATGTTTCTTGAATACCAGAGACGCAA
* * *
222368 TGACTAGCTTCAATCTCTTCATTAGAAACCACATCATGTTGCTCC
317 TGACTACCATCAATCTCTTCAGTAGAAACCACATCATGTTGCTCC
222413 ATGTCTGCTG
Statistics
Matches: 304, Mismatches: 47, Indels: 22
0.82 0.13 0.06
Matches are distributed among these distances:
376 6 0.02
377 10 0.03
378 278 0.91
379 10 0.03
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.34
Consensus pattern (376 bp):
CTCAGCAGGATTAGATTTGTGGCCTTGTTGAAAAGCATTATGTATATCCTCCAGAGATCTCACAT
CGACAACAGGTAATACTGAATTCGTATCTGCATGACCCTGCTAATTCTCAATCATACTAGGAAGA
ATTACTTCCTCAACATCTACCCCTTCATGAAGTTGCTTAAAAACCAAATCAATGCCTTCAACTGA
TCTTGCTTCAAGAACAGGCAGTGCCACCTTGGTCTCCATCTCTATTTCTTCTGTATCATCAAATC
CATCTTTCAGTTCACCAGCAGTATTCACGTATGTTTCTTGAATACCAGAGACGCAATGACTACCA
TCAATCTCTTCAGTAGAAACCACATCATGTTGCTCCTGTTGAATGTAGCAA
Found at i:223472 original size:399 final size:393
Alignment explanation
Indices: 222052--223473 Score: 1252
Period size: 399 Copynumber: 3.6 Consensus size: 393
222042 AATGTAGCAA
* * * *
222052 CTCAGCTGGATTAGATT-TGGTGCCTTGTTGAAAAGCATTATGTATGTCCTCCAGAGATCTTGCA
1 CTCAGCTGGATTAGGTTCTGGTGCCTTGTTGGAAAGCATTATGTATATCCTCCAGAGATCTTGCC
* * * * *
222116 TCGACAACAGGTAAATCTGAATTGGTATCTGCATGACCCTGG-TAATTCTCAATCATGCTAGGAA
66 TCGACAACAGGTAAATCTG-AGTGGTATCTGCATGATCC-GGCTGATTCTCAATCATACTTGGAA
* * * * *
222180 GAATTATTTCCTCAACATCTACTCCTTCATGGAGTTGCTTAAAAGCCAAATCAATGTCTTTCAAT
129 GAATTACTTCCTCAACATCCACTACTTCATGAAGTTGCTTAAAAGCCAAATCAATATC-TTCAAT
** *
222245 GATCTTGCTTCAAGAACAGGCAGCTCCATGTTGGTCTCT--GTCTTCATTTCTTC-GATTTCATC
193 GATCTTGCTTCAAGAACAGGCAGCTCCACATTGGTCTCTGCGT-TTC--TTCTTCTG-TTTCTTC
* * *
222307 AAAGTCATTTTTC-GGTTC-GCTG-GCAGTGTTCAGACTATTTTCTTGAATACCAGAGACGCCA-
254 --A-TCA-TTTTCAGGTTCAACAGAGCA-T-TTCATA--ATTTTCTTGAATACCAGAGA-GCCAT
* * * * *
222368 TGACTAGCTTCAATCTCTTCATTAGAAACCACATCATGTTGCTCCA-TGTCTGCTGATCCATT-T
310 TG-CTAACTTCAATCTCTTCAGTAGAAACTACATCATGCTGCTCTACT-TCTG-TGATCCATTCT
* * * *
222431 CTCAAGTCAGCGGAA-AGAGGCAG
372 -TCAAGTCTG-TGAACTGTGGCAG
* * * * *
222454 CTCCGCTGGTTTAGGTTCTGG-GCATTTTTGGAAAGCATTATGTAGATCCTCCAGAGATCTTGCC
1 CTCAGCTGGATTAGGTTCTGGTGCCTTGTTGGAAAGCATTATGTATATCCTCCAGAGATCTTGCC
* * * * * * * *
222518 TCGACAACTGGTAATTCTGGAGTGAG-ATCTGCATGATCCGACCGATTCTCGATCGTGCTTGTAA
66 TCGACAACAGGTAAATCT-GAGTG-GTATCTGCATGATCCGGCTGATTCTCAATCATACTTGGAA
* * * *
222582 GAATTACTTCCTCAGCATCAAC-ACCGTCATGAAGTTGCTTAAAAGCCAAATCAATATCTTCAGC
129 GAATTACTTCCTCAACATCCACTA-CTTCATGAAGTTGCTTAAAAGCCAAATCAATATCTTCA-A
** * * * * * * * *
222646 CAATCTTGCTTCACGAACAGACTGCTCGACATTGG--TC-GACATCTCTAT-TTCT-TCATATTC
192 TGATCTTGCTTCAAGAACAGGCAGCTCCACATTGGTCTCTG-CGTTTCT-TCTTCTGT-TTCTTC
* * * * * * ** *
222706 AT-TTTTTGA-ATT-AACAGCAGC-TTTC-TCATTTTCTTGAAAACCAGA-AACCAACTCACCAA
254 ATCATTTTCAGGTTCAACAG-AGCATTTCATAATTTTCTTGAATACCAGAGAGCC-A-TTGCTAA
* * * * *
222765 CTTCAATCTCTTCAGTGGAAACCT-CATCATGCTGTTCTACTTCTGTCAACTCATTCCTCAAGT-
316 CTTCAATCTCTTCAGTAGAAA-CTACATCATGCTGCTCTACTTCTGTGATC-CATTCTTCAAGTC
* * *
222828 TTTTAGACTGTAGCAG
379 TGTGA-ACTGTGGCAG
* * * * * *
222844 CTCAACTGGATTAAGTTCTGGT-CCTTTTTGGAGAGCATTATGTATATCCTCCAAAGATTTTGCC
1 CTCAGCTGGATTAGGTTCTGGTGCCTTGTTGGAAAGCATTATGTATATCCTCCAGAGATCTTGCC
* * **
222908 TCGACAAC-GGATAATTCTGAGGTGGGATCTGCATGATCCATCTGATTCTCAATCATACTTGGAA
66 TCGACAACAGG-TAAATCTGA-GTGGTATCTGCATGATCCGGCTGATTCTCAATCATACTTGGAA
* *
222972 GAATTACTTCCTCAACATCCACTCCTCCATGAAGTTGCTTAAAAGCCAAATCAATATCTTCAATC
129 GAATTACTTCCTCAACATCCACTACTTCATGAAGTTGCTTAAAAGCCAAATCAATATCTTCAAT-
* *
223037 GATCTTGCTTCAAGAACATGTAGCTCCA-AGTTGGTCTCTGCGTTTCGTTCTTCTGTTTCTTCAT
193 GATCTTGCTTCAAGAACAGGCAGCTCCACA-TTGGTCTCTGCGTTTC-TTCTTCTGTTTCTTCAT
* * * *
223101 CATTTTCAGGTTCACCAGAAGCATTATCATAACTTTCTTGAATATCAGAGATGGCATTGCTAACT
256 CATTTTCAGGTTCAACAG-AGCATT-TCATAATTTTCTTGAATACCAGAGA-GCCATTGCTAACT
** * * *
223166 TCAATCTCTTTGGAAGAAACTACAACATGCTGCTCTACTTCTGATGATCCGTTCTTCAAGTCTGT
318 TCAATCTCTTCAGTAGAAACTACATCATGCTGCTCTACTTCTG-TGATCCATTCTTCAAGTCTGT
*
223231 GAACTGTGGCGG
382 GAACTGTGGCAG
* * * *
223243 CTGAGCTGGATTAGGTTCT-GTACCTTGTTGCAAAGCATTATGTATATCCTCCAGAGATCTCGCC
1 CTCAGCTGGATTAGGTTCTGGTGCCTTGTTGGAAAGCATTATGTATATCCTCCAGAGATCTTGCC
* * *
223307 TCGACAACAGTTAAATCCGACTTGGTATCTGCATGATCCGGCTGATTCTCAATCATACTTGGAAG
66 TCGACAACAGGTAAATCTGA-GTGGTATCTGCATGATCCGGCTGATTCTCAATCATACTTGGAAG
* *
223372 AATTACTTCCTCAACATCCACTACTTCATGAAGTTGCTTAAAAGCTAAATCAATATCTTCTACTG
130 AATTACTTCCTCAACATCCACTACTTCATGAAGTTGCTTAAAAGCCAAATCAATATCTTC-AATG
*
223437 ATCTTGCTTCAAGAACAGGCAGTTCCACATTGGTCTC
194 ATCTTGCTTCAAGAACAGGCAGCTCCACATTGGTCTC
223474 GTTTTCAATC
Statistics
Matches: 811, Mismatches: 156, Indels: 109
0.75 0.14 0.10
Matches are distributed among these distances:
388 3 0.00
389 12 0.01
390 253 0.31
391 2 0.00
392 7 0.01
393 15 0.02
394 15 0.02
395 2 0.00
396 10 0.01
397 3 0.00
398 7 0.01
399 278 0.34
400 15 0.02
401 8 0.01
402 176 0.22
403 5 0.01
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (393 bp):
CTCAGCTGGATTAGGTTCTGGTGCCTTGTTGGAAAGCATTATGTATATCCTCCAGAGATCTTGCC
TCGACAACAGGTAAATCTGAGTGGTATCTGCATGATCCGGCTGATTCTCAATCATACTTGGAAGA
ATTACTTCCTCAACATCCACTACTTCATGAAGTTGCTTAAAAGCCAAATCAATATCTTCAATGAT
CTTGCTTCAAGAACAGGCAGCTCCACATTGGTCTCTGCGTTTCTTCTTCTGTTTCTTCATCATTT
TCAGGTTCAACAGAGCATTTCATAATTTTCTTGAATACCAGAGAGCCATTGCTAACTTCAATCTC
TTCAGTAGAAACTACATCATGCTGCTCTACTTCTGTGATCCATTCTTCAAGTCTGTGAACTGTGG
CAG
Found at i:225932 original size:24 final size:24
Alignment explanation
Indices: 225900--225945 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
225890 CAATTGCTCC
225900 TGCTTCCTCGTCTCTCTTCTTCGA
1 TGCTTCCTCGTCTCTCTTCTTCGA
*
225924 TGCTTCCTCTTCTCTCTTCTTC
1 TGCTTCCTCGTCTCTCTTCTTC
225946 TTCTACCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.02, C:0.39, G:0.09, T:0.50
Consensus pattern (24 bp):
TGCTTCCTCGTCTCTCTTCTTCGA
Found at i:231052 original size:24 final size:24
Alignment explanation
Indices: 231020--231065 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
231010 CAATTGCTCC
231020 TGCTTCCTCGTCTCTCTTCTTCGA
1 TGCTTCCTCGTCTCTCTTCTTCGA
*
231044 TGCTTCCTCTTCTCTCTTCTTC
1 TGCTTCCTCGTCTCTCTTCTTC
231066 TTCTACCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.02, C:0.39, G:0.09, T:0.50
Consensus pattern (24 bp):
TGCTTCCTCGTCTCTCTTCTTCGA
Found at i:236215 original size:3 final size:3
Alignment explanation
Indices: 236207--236259 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
236197 ACTCTTTGTA
236207 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
236255 TAT TA
1 TAT TA
236260 AGTTTATAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:256331 original size:68 final size:68
Alignment explanation
Indices: 256246--256393 Score: 287
Period size: 68 Copynumber: 2.2 Consensus size: 68
256236 TGCCTGATCT
*
256246 TTAAGAAATGAACTGTTCATAGTTGTTTCTCTATAATATAATTAGCCTTTGCAAGCAATGCTGGT
1 TTAAGAAATGAACTGTTCATAATTGTTTCTCTATAATATAATTAGCCTTTGCAAGCAATGCTGGT
256311 CTG
66 CTG
256314 TTAAGAAATGAACTGTTCATAATTGTTTCTCTATAATATAATTAGCCTTTGCAAGCAATGCTGGT
1 TTAAGAAATGAACTGTTCATAATTGTTTCTCTATAATATAATTAGCCTTTGCAAGCAATGCTGGT
256379 CTG
66 CTG
256382 TTAAGAAATGAA
1 TTAAGAAATGAA
256394 GTTGCAAAGT
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 79 1.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (68 bp):
TTAAGAAATGAACTGTTCATAATTGTTTCTCTATAATATAATTAGCCTTTGCAAGCAATGCTGGT
CTG
Found at i:259751 original size:16 final size:17
Alignment explanation
Indices: 259732--259764 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
259722 GAACCTTTGA
259732 GAAA-TCCTAAAATTTT
1 GAAACTCCTAAAATTTT
*
259748 GAAACTCCTATAATTTT
1 GAAACTCCTAAAATTTT
259765 ATCCTGCAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.39, C:0.15, G:0.06, T:0.39
Consensus pattern (17 bp):
GAAACTCCTAAAATTTT
Found at i:263394 original size:17 final size:17
Alignment explanation
Indices: 263372--263404 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
263362 TGCTCAATTC
263372 TCTTTTCCTTTAACTTG
1 TCTTTTCCTTTAACTTG
*
263389 TCTTTTCGTTTAACTT
1 TCTTTTCCTTTAACTT
263405 TTGGAAGCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.21, G:0.06, T:0.61
Consensus pattern (17 bp):
TCTTTTCCTTTAACTTG
Done.