Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008301.1 Hibiscus syriacus cultivar Beakdansim tig00110987_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: 3376434
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 18
Found at i:2813292 original size:23 final size:22
Alignment explanation
Indices: 2813262--2813305 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
2813252 TTATTTTTTG
2813262 ATTAAATATAAA-TTGTCAATAT
1 ATTAAATATAAAGTTG-CAATAT
2813284 ATTAGAATATAAAGTTGCAATA
1 ATTA-AATATAAAGTTGCAATA
2813306 ATTTATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
23 13 0.65
24 3 0.15
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (22 bp):
ATTAAATATAAAGTTGCAATAT
Found at i:2816258 original size:71 final size:70
Alignment explanation
Indices: 2816082--2816247 Score: 199
Period size: 71 Copynumber: 2.3 Consensus size: 70
2816072 GTAGTTGTGT
* * * *
2816082 ATTTGGACTTTCGGGTTCGTCCACCTTACGTGATTACTTCTGTTTGGTGTGAGTTTAAGATTCCG
1 ATTTGGACTTTTGGGTTCGTCCACCTTACGTGATTACTTCTGTTTGGTGTGAGTTAAACATTCAG
2816147 ATGCG
66 ATGCG
* * * * ** *
2816152 TATTTTGACCTTTGGATTTGTTTACCTTACGTGATTACTTCTGTTTGGTGTGAGTTAAACATTTT
1 -ATTTGGACTTTTGGGTTCGTCCACCTTACGTGATTACTTCTGTTTGGTGTGAGTTAAACA-TTC
2816217 AGTATGC-
64 AG-ATGCG
2816224 ATTTGGACTTTTGGGTTCGTCCAC
1 ATTTGGACTTTTGGGTTCGTCCAC
2816248 ATTATATGAT
Statistics
Matches: 76, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
71 69 0.91
72 3 0.04
73 4 0.05
ACGTcount: A:0.17, C:0.16, G:0.23, T:0.44
Consensus pattern (70 bp):
ATTTGGACTTTTGGGTTCGTCCACCTTACGTGATTACTTCTGTTTGGTGTGAGTTAAACATTCAG
ATGCG
Found at i:2817708 original size:2 final size:2
Alignment explanation
Indices: 2817701--2817753 Score: 63
Period size: 2 Copynumber: 26.5 Consensus size: 2
2817691 TTTATCCAAT
* * *
2817701 TA TA TA TA TA TA TA TA TA TA CA CA CA -A TCA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
2817743 TA TA TA TA TA T
1 TA TA TA TA TA T
2817754 GTAACATGTC
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
1 1 0.02
2 45 0.94
3 2 0.04
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:2819890 original size:34 final size:34
Alignment explanation
Indices: 2819825--2819891 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
2819815 ATTCCAACTA
*
2819825 AATATCTTTTAATTTTCAAATTTAAACAGATAAT
1 AATATCTTTTAATTTTAAAATTTAAACAGATAAT
2819859 AATATCTTTTAA-TTTAAAATATTCAAA-AGATAA
1 AATATCTTTTAATTTTAAAAT-TT-AAACAGATAA
2819892 AGTCACCTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 7 0.23
34 20 0.67
35 3 0.10
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (34 bp):
AATATCTTTTAATTTTAAAATTTAAACAGATAAT
Found at i:2820999 original size:15 final size:16
Alignment explanation
Indices: 2820979--2821044 Score: 91
Period size: 15 Copynumber: 4.1 Consensus size: 16
2820969 CTCGCCTAAC
2820979 GGTATCGATA-TCCTT
1 GGTATCGATACTCCTT
2820994 GGTATCGATA-TCCTT
1 GGTATCGATACTCCTT
2821009 GGTATCGATACTACCTTT
1 GGTATCGATACT-CC-TT
2821027 AGGTATCGATACTCCTT
1 -GGTATCGATACTCCTT
2821044 G
1 G
2821045 AATAACTCAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
15 25 0.53
16 2 0.04
17 4 0.09
18 4 0.09
19 12 0.26
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (16 bp):
GGTATCGATACTCCTT
Found at i:2823495 original size:147 final size:143
Alignment explanation
Indices: 2823205--2823495 Score: 537
Period size: 147 Copynumber: 2.0 Consensus size: 143
2823195 TTCATTCTTT
2823205 ACTTGTTTCATCTCTTAAAATACTTTTCATCTTGGTTTTTCAGTTCCTTAATGATCAATAAGGTT
1 ACTTGTTTCATCTCTTAAAATACTTTTCATCTTGGTTTTTCAGTTCCTTAATGATCAATAAGGTT
2823270 AGCCTAATCTTCAATTCTGTACACAATACCATCTCGTCCATAGACAACCTTGTATCTAAAGCTCG
66 AGCCTAATCTTCAATTCTGTACACAATACCATCTCGTCCATAGACAACCTTGTATCTAAAGCTCG
2823335 TAAGGCTGCAAAC
131 TAAGGCTGCAAAC
*
2823348 ACTTGTTTCAATCTCTTAAAATACTTTTCATCTTTGTTTTTCAGTTCCTTAATTGATCCAATAAG
1 ACTTGTTTC-ATCTCTTAAAATACTTTTCATCTTGGTTTTTCAGTTCCTTAA-TGAT-CAATAAG
2823413 GTTAGCCTAATCTTCAATTCTGTACACAATACCATCTCCGTCCATAGACAACCTTGTATCTAAAG
63 GTTAGCCTAATCTTCAATTCTGTACACAATACCATCT-CGTCCATAGACAACCTTGTATCTAAAG
2823478 CTCGTAAGGCTGCAAAC
127 CTCGTAAGGCTGCAAAC
2823495 A
1 A
2823496 TTTTTCGATT
Statistics
Matches: 143, Mismatches: 1, Indels: 4
0.97 0.01 0.03
Matches are distributed among these distances:
143 9 0.06
144 41 0.29
145 4 0.03
146 44 0.31
147 45 0.31
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.36
Consensus pattern (143 bp):
ACTTGTTTCATCTCTTAAAATACTTTTCATCTTGGTTTTTCAGTTCCTTAATGATCAATAAGGTT
AGCCTAATCTTCAATTCTGTACACAATACCATCTCGTCCATAGACAACCTTGTATCTAAAGCTCG
TAAGGCTGCAAAC
Found at i:2826423 original size:82 final size:83
Alignment explanation
Indices: 2826286--2826456 Score: 260
Period size: 82 Copynumber: 2.0 Consensus size: 83
2826276 CTTGATCTTG
2826286 CACAGGCACTCTCGAATGTGTTTCTTTACCTTGCCTGGCCATGGTAGGTGGAATTACTA-C-TCT
1 CACAGGCACTCTCGAATGTGTTTCTTTACCTTGCCTGGCCATGGTAGGTGGAATTACTACCTTCT
2826349 AGTCTATCATCTCCTGCTT
66 AGTCTATCATCTCC-GCTT
2826368 CACAGGCACTCTCGAATGTGTCTGTCTTTACCTT-CCTGGCCATGGTAGGT-GAATTACTACTCC
1 CACAGGCACTCTCGAATGTGT-T-TCTTTACCTTGCCTGGCCATGGTAGGTGGAATTACTA---C
2826431 CTTCTAGTCTATCATCTCCGCTT
61 CTTCTAGTCTATCATCTCCGCTT
2826454 CAC
1 CAC
2826457 TTCTGGAGCT
Statistics
Matches: 82, Mismatches: 0, Indels: 10
0.89 0.00 0.11
Matches are distributed among these distances:
82 30 0.37
83 17 0.21
84 10 0.12
86 8 0.10
87 17 0.21
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.35
Consensus pattern (83 bp):
CACAGGCACTCTCGAATGTGTTTCTTTACCTTGCCTGGCCATGGTAGGTGGAATTACTACCTTCT
AGTCTATCATCTCCGCTT
Found at i:2833320 original size:14 final size:14
Alignment explanation
Indices: 2833301--2833327 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2833291 CTTGATTTCC
2833301 ATTTTGAAGATGAG
1 ATTTTGAAGATGAG
2833315 ATTTTGAAGATGA
1 ATTTTGAAGATGA
2833328 AAAGGTATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (14 bp):
ATTTTGAAGATGAG
Found at i:2835371 original size:23 final size:23
Alignment explanation
Indices: 2835345--2835390 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2835335 CACCACAGCT
* *
2835345 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTACACCGAAGTGCCA
*
2835368 CGTAGAATTACACCGGAGTGCCA
1 CGTAGAATTACACCGAAGTGCCA
2835391 TATAATAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAATTACACCGAAGTGCCA
Found at i:2842260 original size:23 final size:23
Alignment explanation
Indices: 2842234--2842298 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
2842224 CAACTCGTAT
2842234 AATTGCACCGAAGTGCCATGTAG
1 AATTGCACCGAAGTGCCATGTAG
* **
2842257 AATTGCATC-AGAGTGCCGCGTAG
1 AATTGCACCGA-AGTGCCATGTAG
*
2842280 AATTGCACCGTAGTGCCAT
1 AATTGCACCGAAGTGCCAT
2842299 ATAATAATGT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
22 1 0.03
23 32 0.97
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCATGTAG
Found at i:2844141 original size:31 final size:31
Alignment explanation
Indices: 2844093--2844183 Score: 128
Period size: 31 Copynumber: 2.9 Consensus size: 31
2844083 AAGAGTCGAG
* *
2844093 GGTTACATATGTCCTTCGGGACATATGGACA
1 GGTTACCTACGTCCTTCGGGACATATGGACA
* *
2844124 GTTTACCTACGTCCTTCGGGACATATTGACA
1 GGTTACCTACGTCCTTCGGGACATATGGACA
* *
2844155 GGTTACCTATGTCCTTCGGGATATATGGA
1 GGTTACCTACGTCCTTCGGGACATATGGA
2844184 TAGTGGTAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (31 bp):
GGTTACCTACGTCCTTCGGGACATATGGACA
Found at i:2844213 original size:18 final size:18
Alignment explanation
Indices: 2844187--2844221 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2844177 ATATGGATAG
2844187 TGGTAATTCGGGACAAAA
1 TGGTAATTCGGGACAAAA
*
2844205 TGGTCATTCGGGACAAA
1 TGGTAATTCGGGACAAA
2844222 TTTTAAGTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23
Consensus pattern (18 bp):
TGGTAATTCGGGACAAAA
Found at i:2845751 original size:20 final size:20
Alignment explanation
Indices: 2845726--2845818 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
2845716 TTTTCCCAAT
2845726 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
2845746 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
2845766 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
2845787 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
2845808 TCGCAATGCGA
1 TCGCAATGCGA
2845819 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:2845768 original size:41 final size:41
Alignment explanation
Indices: 2845723--2845818 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
2845713 CGATTTTCCC
2845723 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
2845764 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
2845805 AAATCGCAATGCGA
1 AATTCGCAATGCGA
2845819 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:2845772 original size:21 final size:20
Alignment explanation
Indices: 2845726--2845818 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
2845716 TTTTCCCAAT
*
2845726 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
2845746 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
2845766 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
2845787 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
2845808 TCGCAATGCGA
1 TCGCAATGCGA
2845819 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:2845849 original size:41 final size:41
Alignment explanation
Indices: 2845804--2845881 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
2845794 GCGAATTGGG
* * *
2845804 AAAATCGCAATGCGATACTGACTATT-GCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACT-TTCGCAACGCGATAATAA
*
2845845 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATA
2845882 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 2 0.06
41 30 0.94
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTTTCGCAACGCGATAATAA
Found at i:2845874 original size:20 final size:20
Alignment explanation
Indices: 2845849--2845901 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
2845839 TAATAAAAAA
* *
2845849 TCGCAACGAGATACTTACTT
1 TCGCAACGCGATACTGACTT
2845869 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
2845889 TCGCAACGCGATA
1 TCGCAACGCGATA
2845902 ATACATAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:2846117 original size:22 final size:22
Alignment explanation
Indices: 2846089--2846132 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2846079 CACTCTCTCA
2846089 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
2846111 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
2846133 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:2846419 original size:20 final size:20
Alignment explanation
Indices: 2846394--2846431 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2846384 CGATTCTCTC
2846394 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
2846414 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
2846432 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:2847772 original size:18 final size:18
Alignment explanation
Indices: 2847751--2847795 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
2847741 TCCACTTCGG
*
2847751 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
2847769 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
2847787 GAGCCATCA
1 GAGCCATCA
2847796 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:2848286 original size:20 final size:20
Alignment explanation
Indices: 2848261--2848306 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
2848251 TAGTTTACTT
2848261 TCGCAACAC-GAAAATGACTA
1 TCGCAACACGGAAAATG-CTA
* *
2848281 TCGCAACGCGGAAATTGCTA
1 TCGCAACACGGAAAATGCTA
2848301 TCGCAA
1 TCGCAA
2848307 TGCGAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.37, C:0.26, G:0.20, T:0.17
Consensus pattern (20 bp):
TCGCAACACGGAAAATGCTA
Found at i:2848335 original size:14 final size:14
Alignment explanation
Indices: 2848316--2848404 Score: 88
Period size: 14 Copynumber: 5.8 Consensus size: 14
2848306 ATGCGAAATG
2848316 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
2848330 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
2848346 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
2848362 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
2848378 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
2848394 AAAATCGCAAC
1 AAAATCGCAAC
2848405 ACGAAATGAA
Statistics
Matches: 63, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
14 29 0.46
16 16 0.25
18 18 0.29
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:2848358 original size:32 final size:33
Alignment explanation
Indices: 2848300--2848422 Score: 214
Period size: 32 Copynumber: 3.8 Consensus size: 33
2848290 GGAAATTGCT
*
2848300 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
2848333 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
2848365 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
2848397 ATCGCAACACGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
2848423 TGTGATTTGT
Statistics
Matches: 87, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
32 63 0.72
33 24 0.28
ACGTcount: A:0.48, C:0.24, G:0.18, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:2848458 original size:14 final size:14
Alignment explanation
Indices: 2848439--2848496 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
2848429 TTGTGTTTCG
2848439 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2848453 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
2848469 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
2848485 CGTTGCGATTTT
1 CGTTGCGATTTT
2848497 CCGCGTTGCG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2848470 original size:32 final size:32
Alignment explanation
Indices: 2848434--2848495 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
2848424 GTGATTTGTG
2848434 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
2848466 TTTCGCGTTGCGATTTTGTCGTTGCGATTT
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTT
2848496 TCCGCGTTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.08, C:0.18, G:0.26, T:0.48
Consensus pattern (32 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
Found at i:2848522 original size:48 final size:46
Alignment explanation
Indices: 2848439--2848530 Score: 132
Period size: 48 Copynumber: 2.0 Consensus size: 46
2848429 TTGTGTTTCG
* *
2848439 CGTTGCGATTTTGTCGTTGCGATTTCATTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTGTCGTTGCGATGTCATTTCGCGTTGCAATTTTGT
2848485 CGTTGCGATTTTCCG-CGTTGCGATAGTCATTTCGCGTTGCAATTTT
1 CGTTGCGATTTT--GTCGTTGCGAT-GTCATTTCGCGTTGCAATTTT
2848531 AAGTTGCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
46 12 0.29
47 9 0.22
48 20 0.49
ACGTcount: A:0.11, C:0.20, G:0.25, T:0.45
Consensus pattern (46 bp):
CGTTGCGATTTTGTCGTTGCGATGTCATTTCGCGTTGCAATTTTGT
Found at i:2850685 original size:7 final size:7
Alignment explanation
Indices: 2850669--2850706 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
2850659 GTCAAAGAAA
*
2850669 GTCAATG
1 GTCAACG
2850676 GTCAACG
1 GTCAACG
2850683 GTCAACG
1 GTCAACG
2850690 GTCAACG
1 GTCAACG
2850697 GTCAACG
1 GTCAACG
2850704 GTC
1 GTC
2850707 GGGTCGGGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:2850713 original size:5 final size:5
Alignment explanation
Indices: 2850703--2850743 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
2850693 AACGGTCAAC
*
2850703 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC
2850744 AACGGTCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 28 0.88
7 4 0.12
ACGTcount: A:0.05, C:0.22, G:0.54, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:2850724 original size:22 final size:22
Alignment explanation
Indices: 2850696--2850750 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
2850686 AACGGTCAAC
2850696 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
2850718 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
2850740 GGTCAACGGTC
1 GGTCAACGGTC
2850751 AAACCGATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.11, C:0.24, G:0.47, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:2850770 original size:19 final size:18
Alignment explanation
Indices: 2850746--2850864 Score: 96
Period size: 19 Copynumber: 6.2 Consensus size: 18
2850736 GTCGGGTCAA
2850746 CGGTCAAACCGATTCAGAC
1 CGGTCAAACCG-TTCAGAC
2850765 CGGTCAAACCGGTTC-GAAC
1 CGGTCAAACC-GTTCAG-AC
* * *
2850784 CGGTTGAAACCGGTCAAAC
1 CGG-TCAAACCGTTCAGAC
* *
2850803 CGGTCAGAACCGGTTGAAAC
1 CGGTCA-AACC-GTTCAGAC
*
2850823 CGGTCAAACCGGTCAGAAC
1 CGGTCAAACCGTTCAG-AC
*
2850842 CGGTCAAACCGGTCAGAAC
1 CGGTCAAACCGTTCAG-AC
2850861 CGGT
1 CGGT
2850865 TGAAAACCGG
Statistics
Matches: 84, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
18 6 0.07
19 59 0.70
20 19 0.23
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.14
Consensus pattern (18 bp):
CGGTCAAACCGTTCAGAC
Found at i:2850853 original size:48 final size:48
Alignment explanation
Indices: 2850746--2850884 Score: 176
Period size: 48 Copynumber: 2.9 Consensus size: 48
2850736 GTCGGGTCAA
* * * *
2850746 CGGTCAAACCGATTCAG-ACCGG-TCAAACCGGTTCGAACCGGTTGAAAC
1 CGGTCAAACCG-GTCAGAACCGGTTGAAACCGG-TCAAACCGGTAGAAAC
2850794 CGGTCAAACCGGTCAGAACCGGTTGAAACCGGTCAAACCGGTCAG-AAC
1 CGGTCAAACCGGTCAGAACCGGTTGAAACCGGTCAAACCGGT-AGAAAC
*
2850842 CGGTCAAACCGGTCAGAACCGGTTGAAAACCGGTTAAACCGGT
1 CGGTCAAACCGGTCAGAACCGGTTG-AAACCGGTCAAACCGGT
2850885 TTCCAGCAGC
Statistics
Matches: 82, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
47 4 0.05
48 53 0.65
49 25 0.30
ACGTcount: A:0.30, C:0.28, G:0.27, T:0.15
Consensus pattern (48 bp):
CGGTCAAACCGGTCAGAACCGGTTGAAACCGGTCAAACCGGTAGAAAC
Found at i:2850861 original size:29 final size:29
Alignment explanation
Indices: 2850746--2850864 Score: 56
Period size: 29 Copynumber: 4.1 Consensus size: 29
2850736 GTCGGGTCAA
* *
2850746 CGGTCAAACCGATTCAG-ACCGGT-CAAAC
1 CGGTCAAACCG-GTCAGAACCGGTAGAAAC
* * *
2850774 CGGTTCGAACCGGT-TGAAACCGGT-CAAAC
1 CGG-TCAAACCGGTCAG-AACCGGTAGAAAC
* *
2850803 CGGTCAGAACCGGT-TGAAACCGGT-CAAAC
1 CGGTCA-AACCGGTCAG-AACCGGTAGAAAC
2850832 CGGTCAGAACCGGTCA-AACCGGTCAG-AAC
1 CGGTCA-AACCGGTCAGAACCGGT-AGAAAC
2850861 CGGT
1 CGGT
2850865 TGAAAACCGG
Statistics
Matches: 78, Mismatches: 6, Indels: 13
0.80 0.06 0.13
Matches are distributed among these distances:
27 1 0.01
28 13 0.17
29 64 0.82
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.14
Consensus pattern (29 bp):
CGGTCAAACCGGTCAGAACCGGTAGAAAC
Found at i:2850874 original size:11 final size:9
Alignment explanation
Indices: 2850763--2850885 Score: 102
Period size: 10 Copynumber: 12.8 Consensus size: 9
2850753 ACCGATTCAG
*
2850763 ACCGGTCAA
1 ACCGGTTAA
*
2850772 ACCGGTTCGA
1 ACCGGTT-AA
2850782 ACCGGTTGAA
1 ACCGGTT-AA
*
2850792 ACCGGTCAA
1 ACCGGTTAA
*
2850801 ACCGGTCAGA
1 ACCGGTTA-A
2850811 ACCGGTTGAA
1 ACCGGTT-AA
*
2850821 ACCGGTCAA
1 ACCGGTTAA
*
2850830 ACCGGTCAGA
1 ACCGGTTA-A
*
2850840 ACCGGTCAA
1 ACCGGTTAA
*
2850849 ACCGGTCAGA
1 ACCGGTTA-A
2850859 ACCGGTTGAAA
1 ACCGGTT--AA
2850870 ACCGGTTAA
1 ACCGGTTAA
2850879 ACCGGTT
1 ACCGGTT
2850886 TCCAGCAGCC
Statistics
Matches: 99, Mismatches: 8, Indels: 14
0.82 0.07 0.12
Matches are distributed among these distances:
9 44 0.44
10 45 0.45
11 9 0.09
12 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.27, T:0.15
Consensus pattern (9 bp):
ACCGGTTAA
Found at i:2858056 original size:5 final size:5
Alignment explanation
Indices: 2858046--2858103 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
2858036 AACGGTCAAC
* *
2858046 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG
2858095 GGTCG GGTC
1 GGTCG GGTC
2858104 AACGGTCAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.07, C:0.22, G:0.52, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:2858066 original size:7 final size:7
Alignment explanation
Indices: 2858019--2858049 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
2858009 GTCAAAGAAA
*
2858019 GTCAATG
1 GTCAACG
2858026 GTCAACG
1 GTCAACG
2858033 GTCAACG
1 GTCAACG
2858040 GTCAACG
1 GTCAACG
2858047 GTC
1 GTC
2858050 GGGTCGGGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:2858074 original size:22 final size:22
Alignment explanation
Indices: 2858032--2858110 Score: 131
Period size: 22 Copynumber: 3.5 Consensus size: 22
2858022 AATGGTCAAC
*
2858032 GGTCAACGGTCAACGGTCGGGTCG
1 GGTCAACGGTC--GGGTCGGGTCG
2858056 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
2858078 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
2858100 GGTCAACGGTC
1 GGTCAACGGTC
2858111 AAACCGATTC
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
22 43 0.80
24 11 0.20
ACGTcount: A:0.13, C:0.24, G:0.46, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:2858110 original size:17 final size:17
Alignment explanation
Indices: 2858039--2858076 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
2858029 AACGGTCAAC
2858039 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
2858056 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
2858073 GGTC
1 GGTC
2858077 GGGTCAACGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.11, C:0.24, G:0.47, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:2858145 original size:19 final size:19
Alignment explanation
Indices: 2858106--2858197 Score: 73
Period size: 19 Copynumber: 4.7 Consensus size: 19
2858096 GTCGGGTCAA
*
2858106 CGGTCAAACCGATTC-AGAC
1 CGGTCAAACCGGTTCGA-AC
2858125 CGGTCAAACCGGTTCGAAC
1 CGGTCAAACCGGTTCGAAC
* *
2858144 CGGTTGAAACCGG-TCAAAC
1 CGG-TCAAACCGGTTCGAAC
*
2858163 CAGTCAGAACCGGTT-GAAAAC
1 CGGTCA-AACCGGTTCG--AAC
*
2858184 CGGTTAAACCGGTT
1 CGGTCAAACCGGTT
2858198 TCCAGCAGCC
Statistics
Matches: 59, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
18 2 0.03
19 32 0.54
20 18 0.31
21 7 0.12
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.17
Consensus pattern (19 bp):
CGGTCAAACCGGTTCGAAC
Found at i:2858155 original size:29 final size:31
Alignment explanation
Indices: 2858123--2858197 Score: 111
Period size: 29 Copynumber: 2.5 Consensus size: 31
2858113 ACCGATTCAG
2858123 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
2858152 ACCGGTCAAACCAG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
2858182 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
2858198 TCCAGCAGCC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
28 2 0.05
29 23 0.57
30 14 0.35
31 1 0.03
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:2858197 original size:9 final size:9
Alignment explanation
Indices: 2858123--2858197 Score: 60
Period size: 9 Copynumber: 7.8 Consensus size: 9
2858113 ACCGATTCAG
*
2858123 ACCGGTCAA
1 ACCGGTTAA
*
2858132 ACCGGTTCGA
1 ACCGGTT-AA
2858142 ACCGGTTGAA
1 ACCGGTT-AA
*
2858152 ACCGGTCAA
1 ACCGGTTAA
* *
2858161 ACCAGTCAGA
1 ACCGGTTA-A
2858171 ACCGGTTGAAA
1 ACCGGTT--AA
2858182 ACCGGTTAA
1 ACCGGTTAA
2858191 ACCGGTT
1 ACCGGTT
2858198 TCCAGCAGCC
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
9 24 0.44
10 21 0.39
11 8 0.15
12 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (9 bp):
ACCGGTTAA
Found at i:2860330 original size:19 final size:19
Alignment explanation
Indices: 2860308--2860375 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
2860298 ATCGCAACGA
2860308 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
2860327 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
2860346 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
2860360 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
2860376 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:2860451 original size:20 final size:20
Alignment explanation
Indices: 2860394--2860451 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
2860384 TCGCATTGCG
* *
2860394 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
2860414 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
2860434 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
2860452 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:2861537 original size:24 final size:24
Alignment explanation
Indices: 2861510--2861563 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2861500 GTATTCGAAA
* *
2861510 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
2861534 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
2861558 TTTGAT
1 TTTGAT
2861564 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:2864077 original size:14 final size:14
Alignment explanation
Indices: 2864058--2864114 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2864048 GCGAAATGAA
2864058 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2864072 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
2864091 AATCGCAACGAGGG
1 AATCGCAACGAGAG
2864105 AATCGCAACG
1 AATCGCAACG
2864115 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.21, G:0.26, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2864082 original size:33 final size:33
Alignment explanation
Indices: 2864040--2864133 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
2864030 GGAAATTACT
2864040 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
2864073 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
2864106 ATCGCAACGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
2864134 CGAATTTAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:2864148 original size:19 final size:19
Alignment explanation
Indices: 2864020--2864137 Score: 85
Period size: 19 Copynumber: 6.7 Consensus size: 19
2864010 CTTAATGTCC
* **
2864020 ATCGCAACGCGGAAATTACT
1 ATCGCAACGC-GAAATGAAA
*
2864040 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
2864059 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
2864073 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
**
2864092 ATCGCAA--CG--A-GGGA
1 ATCGCAACGCGAAATGAAA
2864106 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
2864125 ATCGCAACGCGAA
1 ATCGCAACGCGAA
2864138 TTTAATTTCG
Statistics
Matches: 78, Mismatches: 10, Indels: 21
0.72 0.09 0.19
Matches are distributed among these distances:
14 19 0.24
15 2 0.03
16 4 0.05
17 4 0.05
18 2 0.03
19 38 0.49
20 9 0.12
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:2864155 original size:19 final size:20
Alignment explanation
Indices: 2864133--2864175 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2864123 AAATCGCAAC
2864133 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
2864152 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
2864172 GCGA
1 GCGA
2864176 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:2864160 original size:14 final size:14
Alignment explanation
Indices: 2864161--2864194 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2864151 TGCGATTTTC
2864161 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
2864175 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
2864189 ATTTTC
1 ATTTTC
2864195 ATTTTGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:2864335 original size:14 final size:14
Alignment explanation
Indices: 2864316--2864352 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2864306 CATCAATTAA
2864316 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2864330 ACAAATCACCTTTT
1 ACAAATCAACTTTT
2864344 ACAAATCAA
1 ACAAATCAA
2864353 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2867330 original size:20 final size:19
Alignment explanation
Indices: 2867295--2867438 Score: 65
Period size: 20 Copynumber: 7.9 Consensus size: 19
2867285 TCTTTTGGTT
*
2867295 GAAATGAAAATTGCAACGA
1 GAAATGAAAATCGCAACGA
* *
2867314 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
2867335 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
2867354 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
2867368 GAAATGACTATCG---CGA
1 GAAATGAAAATCGCAACGA
** * *
2867384 -CCA-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
2867401 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGA
*
2867421 GAAATAAAAATCGCAACG
1 GAAATGAAAATCGCAACG
2867439 CGTTGCGATT
Statistics
Matches: 94, Mismatches: 18, Indels: 26
0.68 0.13 0.19
Matches are distributed among these distances:
14 17 0.18
15 1 0.01
16 4 0.04
17 4 0.04
18 1 0.01
19 19 0.20
20 46 0.49
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:2867377 original size:33 final size:33
Alignment explanation
Indices: 2867320--2867418 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
2867310 ACGAGATAAT
*
2867320 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
2867354 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
2867387 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
2867419 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:2868095 original size:20 final size:20
Alignment explanation
Indices: 2868002--2868095 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
2867992 CGCTATGTAA
*
2868002 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
2868022 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
2868042 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
2868063 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
2868083 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
2868096 TTTCCCAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:2868114 original size:41 final size:41
Alignment explanation
Indices: 2868023--2868157 Score: 130
Period size: 41 Copynumber: 3.3 Consensus size: 41
2868013 AAAGTCAGTA
* * * ** *
2868023 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
2868063 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* ** *
2868105 TCGCGTTGCGAT-TTACTTATTCGCATTGCGAATTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
2868146 TCGCGTTGCGAT
1 TCGCGTTGCGAT
2868158 TTACTTATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.04
41 73 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:2868128 original size:20 final size:20
Alignment explanation
Indices: 2868084--2868176 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
2868074 ATAGTCAGTA
* **
2868084 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
2868105 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
2868125 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
2868146 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
2868166 TCGCATTGCGA
1 TCGCATTGCGA
2868177 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:2868158 original size:41 final size:41
Alignment explanation
Indices: 2868084--2868179 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
2868074 ATAGTCAGTA
*
2868084 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
2868125 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
2868166 TCGCATTGCGAATT
1 TCGCATTGCGAATT
2868180 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:2869061 original size:20 final size:20
Alignment explanation
Indices: 2869036--2869210 Score: 199
Period size: 20 Copynumber: 8.6 Consensus size: 20
2869026 TAGTTGAAAA
2869036 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
2869056 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
** * *
2869076 TCGCGTTGCGATAGTCTATAG
1 TCGCGTTGCGATTTTCCAT-T
2869097 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * *
2869117 TCGCGTTGCGATAGTCTACA-G
1 TCGCGTTGCGAT--TTTCCATT
2869138 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** *
2869158 TCGCGTTGCGATAGTTGAAAT
1 TCGCGTTGCGAT-TTTCCATT
*
2869179 TCGCGTTGCGATTTTCTATT
1 TCGCGTTGCGATTTTCCATT
2869199 TCGCGTTGCGAT
1 TCGCGTTGCGAT
2869211 AGTCTACAGT
Statistics
Matches: 128, Mismatches: 22, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
19 4 0.03
20 76 0.59
21 44 0.34
22 4 0.03
ACGTcount: A:0.14, C:0.22, G:0.24, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:2869101 original size:41 final size:41
Alignment explanation
Indices: 2869056--2869279 Score: 328
Period size: 41 Copynumber: 5.4 Consensus size: 41
2869046 ATTTTCCATT
*
2869056 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTATAG
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAG
2869097 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAG
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAG
* *
2869138 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAAAT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCT-ACAG
*
2869179 TCGCGTTGCGATTTTCTATTTCGCGTTGCGATAGTCTACAG
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAG
* *
2869220 TTGTCGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAG
1 TCG-CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTCTACAG
*
2869261 TTGTCGTTGCGATTTTCCA
1 TCG-CGTTGCGATTTTCCA
2869280 AATTCGTTGT
Statistics
Matches: 170, Mismatches: 9, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
40 2 0.01
41 151 0.89
42 14 0.08
43 3 0.02
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAG
Found at i:2869184 original size:123 final size:124
Alignment explanation
Indices: 2869055--2869279 Score: 366
Period size: 123 Copynumber: 1.8 Consensus size: 124
2869045 GATTTTCCAT
* *
2869055 TTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTATAGTCG-CGTTGCGATTTTCC-ATTT
1 TTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGTCGTTGCGATTTTCCAAATT
2869118 CGCGTTGCGATAGTCTACAGTCG-CGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
66 --CGTTGCGATAGTCTACAGTCGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
* *
2869178 TTCGCGTTGCGATTTTCTATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 TTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGTCGTTGCGATTTTCCAAATT
*
2869243 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCA
66 CGTTGCGATAGTCTACAGTCGTCGTTGCGATTTTCCA
2869280 AATTCGTTGT
Statistics
Matches: 94, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
123 62 0.66
124 29 0.31
125 3 0.03
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.40
Consensus pattern (124 bp):
TTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGTCGTTGCGATTTTCCAAATT
CGTTGCGATAGTCTACAGTCGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAA
Found at i:2869230 original size:22 final size:22
Alignment explanation
Indices: 2869202--2869273 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
2869192 TTCTATTTCG
2869202 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
2869224 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
2869243 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
2869265 CGTTGCGAT
1 CGTTGCGAT
2869274 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 5 0.13
22 19 0.49
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:2869247 original size:19 final size:19
Alignment explanation
Indices: 2869223--2869288 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
2869213 TCTACAGTTG
2869223 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
2869242 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
2869263 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
2869283 TCGTTG
1 TCGTTG
2869289 TGATAGTTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 16 0.44
20 5 0.14
21 5 0.14
22 10 0.28
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:2869247 original size:61 final size:60
Alignment explanation
Indices: 2869012--2869251 Score: 218
Period size: 61 Copynumber: 3.9 Consensus size: 60
2869002 TTCGCGTTGC
* * * *
2869012 ATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATTTTCC
1 ATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTCCAATTC-CGTTGCGATTTTCT
* * **
2869073 ATTTCGCGTTGCGATAGTCTATAGTCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCT
1 ATTTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCAATTC-CGTTGCGATTTTCT
** * * * * **
2869134 ACAGTCGCGTTGCGAT--TTTCCATTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTCT
1 A-TTTCGCGTTGCGATAGTCTACA-GTCGCGTTGCGAT-TTTCCAATTC-CGTTGCGATTTTCT
*
2869196 ATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT-CGTTGCGAT
1 ATTTCGCGTTGCGATAGTCTACAGTCG-CGTTGCGATTTTCC-AATTCCGTTGCGAT
2869252 AGTCTACAGT
Statistics
Matches: 145, Mismatches: 26, Indels: 16
0.78 0.14 0.09
Matches are distributed among these distances:
60 3 0.02
61 88 0.61
62 37 0.26
63 17 0.12
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.39
Consensus pattern (60 bp):
ATTTCGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCAATTCCGTTGCGATTTTCT
Found at i:2869383 original size:6 final size:6
Alignment explanation
Indices: 2869372--2869409 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
2869362 GACACGTATT
2869372 ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
2869410 CGAGACGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.32, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2869912 original size:5 final size:5
Alignment explanation
Indices: 2869904--2869964 Score: 86
Period size: 5 Copynumber: 11.6 Consensus size: 5
2869894 CCGTCTCGTC
*
2869904 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCTGG TCGGG TCGTGG TCGTGG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG
2869956 TCGTGG TCG
1 TCG-GG TCG
2869965 TGGTAATACG
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
5 36 0.68
6 17 0.32
ACGTcount: A:0.00, C:0.20, G:0.54, T:0.26
Consensus pattern (5 bp):
TCGGG
Found at i:2878346 original size:30 final size:30
Alignment explanation
Indices: 2878312--2878423 Score: 163
Period size: 30 Copynumber: 3.7 Consensus size: 30
2878302 GTTGAACATT
* *
2878312 AAATACAAAAAGTTAAAGGACCAAAATAGA
1 AAATACAAAAACTTAAAGGACTAAAATAGA
*
2878342 AAATACAAAAACTTAAAGGACTAAAATAGCT
1 AAATACAAAAACTTAAAGGACTAAAATAG-A
*
2878373 AAA-ACAAAAAGTTAAAGGACTAAAATAGA
1 AAATACAAAAACTTAAAGGACTAAAATAGA
*
2878402 AAATAAAAAAACTTAAAGGACT
1 AAATACAAAAACTTAAAGGACT
2878424 CAACCAGTAA
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
29 3 0.04
30 67 0.92
31 3 0.04
ACGTcount: A:0.62, C:0.10, G:0.12, T:0.16
Consensus pattern (30 bp):
AAATACAAAAACTTAAAGGACTAAAATAGA
Found at i:2878436 original size:30 final size:30
Alignment explanation
Indices: 2878311--2878439 Score: 161
Period size: 30 Copynumber: 4.3 Consensus size: 30
2878301 GGTTGAACAT
* *
2878311 TAAATACAAAAAGTTAAAGGACCAAAATAG
1 TAAATACAAAAACTTAAAGGACTAAAATAG
*
2878341 AAAATACAAAAACTTAAAGGACTAAAATAG
1 TAAATACAAAAACTTAAAGGACTAAAATAG
*
2878371 CTAAA-ACAAAAAGTTAAAGGACTAAAATAG
1 -TAAATACAAAAACTTAAAGGACTAAAATAG
* * * **
2878401 AAAATAAAAAAACTTAAAGGACTCAACCAG
1 TAAATACAAAAACTTAAAGGACTAAAATAG
2878431 TAAATACAA
1 TAAATACAA
2878440 CAAATCAGAG
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
29 3 0.04
30 78 0.93
31 3 0.04
ACGTcount: A:0.61, C:0.12, G:0.11, T:0.16
Consensus pattern (30 bp):
TAAATACAAAAACTTAAAGGACTAAAATAG
Found at i:2879987 original size:3 final size:3
Alignment explanation
Indices: 2879969--2880020 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
2879959 ATATATGATT
*
2879969 TAA TAA -AA AAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
2880016 TAA TA
1 TAA TA
2880021 TTTTTGGTAG
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
2 4 0.09
3 38 0.84
4 3 0.07
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:2880445 original size:40 final size:40
Alignment explanation
Indices: 2880384--2880459 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
2880374 CAGGTTATCT
*
2880384 AGGGGGTGACAAGGCTCCTACGTAATGAGGA-GGTATGGA
1 AGGGGGTGACAAGGATCCTACGTAATGAGGACGGTATGGA
* *
2880423 AGGGGGATGACATGGATCCTACGTGATGAGGACGGTA
1 AGGGGG-TGACAAGGATCCTACGTAATGAGGACGGTA
2880460 GGCCATCTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 6 0.19
40 22 0.69
41 4 0.12
ACGTcount: A:0.28, C:0.13, G:0.41, T:0.18
Consensus pattern (40 bp):
AGGGGGTGACAAGGATCCTACGTAATGAGGACGGTATGGA
Found at i:2880461 original size:132 final size:132
Alignment explanation
Indices: 2880295--2880550 Score: 354
Period size: 132 Copynumber: 1.9 Consensus size: 132
2880285 TCCGGTCGGA
* *
2880295 GGATGACACGGTTCCTACGTGATGAGAACGGTAGGCCATCTTTA-GAA-ATGATAACACGGTTCC
1 GGATGACACGGATCCTACGTGATGAGAACGGTAGGCCATCTTTAGGAAGATGATAACACGATTCC
*
2880358 TACGTGATGAGGACGACAGGTTATCTAGGGGGTGACAAGGCTCCTACGTAATGAGGAGGTATGGA
66 TACGCGATGAGGACGACAGGTTATC-A-GGGGTGACAAGGCTCCTACGTAATGAGGAGGTATGGA
2880423 AGGG
129 AGGG
* * * *
2880427 GGATGACATGGATCCTACGTGATGAGGACGGTAGGCCATCTTTAGGAAGGGTGATAACTCGATTC
1 GGATGACACGGATCCTACGTGATGAGAACGGTAGGCCATCTTTAGGAA-GATGATAACACGATTC
* * * * * *
2880492 CTATGCGATGAGGATGGCTGGTTATCAGGGGTGACACGGCTCCTACGTATTGAGGAGGT
65 CTACGCGATGAGGACGACAGGTTATCAGGGGTGACAAGGCTCCTACGTAATGAGGAGGT
2880551 CTAGTCGGGG
Statistics
Matches: 108, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
132 41 0.38
133 33 0.31
134 1 0.01
135 33 0.31
ACGTcount: A:0.26, C:0.17, G:0.34, T:0.23
Consensus pattern (132 bp):
GGATGACACGGATCCTACGTGATGAGAACGGTAGGCCATCTTTAGGAAGATGATAACACGATTCC
TACGCGATGAGGACGACAGGTTATCAGGGGTGACAAGGCTCCTACGTAATGAGGAGGTATGGAAG
GG
Found at i:2880579 original size:133 final size:131
Alignment explanation
Indices: 2880289--2880587 Score: 350
Period size: 133 Copynumber: 2.3 Consensus size: 131
2880279 AAGAGGTCCG
*
2880289 GTCGGAGGATGACACGGTTCCTACGTGATGAGAACGGTAGGCCATCTTTAGAAATGATAACACGG
1 GTCGG-GGATGACACGGTTCCTACGTGATGAGAACGGTAGGCCATCTTTAGAAATGATAACACGA
*
2880354 TTCCTACGTGATGAGGACGACAGGTTATCTAGGGGGTGACAAGGCTCCTACGTAATGAGGAGGTA
65 TTCCTACGCGATGAGGACGACAGGTTATCTAGGGGGTGACAAGGCTCCTACGTAATGAGGAGGTA
*
2880419 TG
130 TA
** * * * * *
2880421 GAAGGGGGATGACATGGATCCTACGTGATGAGGACGGTAGGCCATCTTTAGGAAGGGTGATAACT
1 G-TCGGGGATGACACGGTTCCTACGTGATGAGAACGGTAGGCCATCTTTA-GAA--ATGATAACA
* * * * * *
2880486 CGATTCCTATGCGATGAGGATGGCTGGTTATC-A-GGGGTGACACGGCTCCTACGTATTGAGGAG
62 CGATTCCTACGCGATGAGGACGACAGGTTATCTAGGGGGTGACAAGGCTCCTACGTAATGAGGAG
*
2880549 GTCTA
127 GTATA
** *
2880554 GTCGGGGAATGACACGGTTTATACGTGATTAGAA
1 GTCGGGG-ATGACACGGTTCCTACGTGATGAGAA
2880588 TGGAAGATCG
Statistics
Matches: 137, Mismatches: 25, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
132 46 0.34
133 57 0.42
134 1 0.01
135 33 0.24
ACGTcount: A:0.26, C:0.16, G:0.34, T:0.24
Consensus pattern (131 bp):
GTCGGGGATGACACGGTTCCTACGTGATGAGAACGGTAGGCCATCTTTAGAAATGATAACACGAT
TCCTACGCGATGAGGACGACAGGTTATCTAGGGGGTGACAAGGCTCCTACGTAATGAGGAGGTAT
A
Found at i:2880833 original size:66 final size:65
Alignment explanation
Indices: 2880720--2880846 Score: 204
Period size: 66 Copynumber: 1.9 Consensus size: 65
2880710 TGTTTCGAGG
*
2880720 GAAACAGACTCAAAGATTTTTTCTCAAAAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCCAT
1 GAAACAGACTCAAAGATTTTTTCTCAAAAGAAATTATCTCAAGAGAGACAAAA-TTTGTTTCCAT
2880785 A
65 A
2880786 GAAACAGACTCAAAGATTGTTTTTCTCAAAAGAAATTATCTC-A-AGAGACAAAATTTGTTTC
1 GAAACAGACTCAAAGA-T-TTTTTCTCAAAAGAAATTATCTCAAGAGAGACAAAATTTGTTTC
2880847 AAGACAAACA
Statistics
Matches: 58, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
65 8 0.14
66 26 0.45
67 2 0.03
68 22 0.38
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (65 bp):
GAAACAGACTCAAAGATTTTTTCTCAAAAGAAATTATCTCAAGAGAGACAAAATTTGTTTCCATA
Found at i:2886029 original size:30 final size:30
Alignment explanation
Indices: 2885995--2886101 Score: 117
Period size: 30 Copynumber: 3.6 Consensus size: 30
2885985 GCTAAACAAT
*
2885995 AAATACATAAAGTTAAAGGACCAAAATAGC
1 AAATACATAAACTTAAAGGACCAAAATAGC
* *
2886025 AAATACAAAAACTTAAAGGA-CTAAATAGC
1 AAATACATAAACTTAAAGGACCAAAATAGC
* * * * * *
2886054 TAAAAATAGAAAGTTAAAGGACTAAAATAGA
1 -AAATACATAAACTTAAAGGACCAAAATAGC
2886085 AAATACATAAACTTAAA
1 AAATACATAAACTTAAA
2886102 AGACTCAACC
Statistics
Matches: 61, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
29 8 0.13
30 47 0.77
31 6 0.10
ACGTcount: A:0.60, C:0.10, G:0.11, T:0.19
Consensus pattern (30 bp):
AAATACATAAACTTAAAGGACCAAAATAGC
Found at i:2886398 original size:107 final size:107
Alignment explanation
Indices: 2886212--2886422 Score: 368
Period size: 107 Copynumber: 2.0 Consensus size: 107
2886202 GAAATAAAAA
* *
2886212 AACAAATAAAGATTACAAACCAAAATACAATGGTCAAAATGAGAGTTCCTGAGAATTACAAGGAC
1 AACAAATAAAGATTACAAACCAAAATACAATGGTCAAAATGAGAGTACCTGAAAATTACAAGGAC
*
2886277 TAACATGATAATAACAACAACAACTAAAAGGGCTACACATTT
66 TAAAATGATAATAACAACAACAACTAAAAGGGCTACACATTT
*
2886319 AACAAATGAAGATTACAAACCAAAATACAATGGTCAAAATGAGAGTACCTGAAAATTACAAGGAC
1 AACAAATAAAGATTACAAACCAAAATACAATGGTCAAAATGAGAGTACCTGAAAATTACAAGGAC
* *
2886384 TAAAATGATAATAACAACAATAATTAAAAGGGCTACACA
66 TAAAATGATAATAACAACAACAACTAAAAGGGCTACACA
2886423 GTAATTACAA
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
107 98 1.00
ACGTcount: A:0.52, C:0.16, G:0.13, T:0.19
Consensus pattern (107 bp):
AACAAATAAAGATTACAAACCAAAATACAATGGTCAAAATGAGAGTACCTGAAAATTACAAGGAC
TAAAATGATAATAACAACAACAACTAAAAGGGCTACACATTT
Found at i:2890773 original size:25 final size:25
Alignment explanation
Indices: 2890726--2890773 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2890716 TAATTAGTTA
* * *
2890726 ATAAGTAAATAATGATTTTTTTAAG
1 ATAAATAAATAATGAATTGTTTAAG
2890751 ATAAATAAATAATGAATTGTTTA
1 ATAAATAAATAATGAATTGTTTA
2890774 GTTTTCCATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (25 bp):
ATAAATAAATAATGAATTGTTTAAG
Found at i:2903296 original size:20 final size:20
Alignment explanation
Indices: 2903271--2903331 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
2903261 TTTTGGTGCA
*
2903271 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
* *
2903291 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATACCCCC-AT
*
2903312 GAATGGGAACCGATTCCCCC
1 G-A-GGGAACCGATACCCCC
2903332 CACAGGGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 16 0.46
21 2 0.06
22 1 0.03
23 16 0.46
ACGTcount: A:0.25, C:0.33, G:0.25, T:0.18
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:2906142 original size:20 final size:20
Alignment explanation
Indices: 2906113--2906150 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2906103 ATTTTACACT
2906113 TAGGGAACCGATTCCCCCTA
1 TAGGGAACCGATTCCCCCTA
*
2906133 TAGGGTACCGATTCCCCC
1 TAGGGAACCGATTCCCCC
2906151 CACGCTCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.37, G:0.21, T:0.21
Consensus pattern (20 bp):
TAGGGAACCGATTCCCCCTA
Found at i:2909670 original size:23 final size:23
Alignment explanation
Indices: 2909644--2909688 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
2909634 GAATCGATAC
2909644 CCCTTTGAAGGGGAACCGATTCG
1 CCCTTTGAAGGGGAACCGATTCG
*
2909667 CCCTTTGAATGGGAACCGATTC
1 CCCTTTGAAGGGGAACCGATTC
2909689 CCCCCTTAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
CCCTTTGAAGGGGAACCGATTCG
Found at i:2909719 original size:20 final size:21
Alignment explanation
Indices: 2909677--2909719 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2909667 CCCTTTGAAT
* *
2909677 GGGAACCGATTCCCCCCTTAG
1 GGGAACCGATACCCCCCTAAG
*
2909698 GGGAATCGATACCCCCC-AAG
1 GGGAACCGATACCCCCCTAAG
2909718 GG
1 GG
2909720 TTCTGGATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.23, C:0.35, G:0.28, T:0.14
Consensus pattern (21 bp):
GGGAACCGATACCCCCCTAAG
Found at i:2910432 original size:21 final size:22
Alignment explanation
Indices: 2910397--2910439 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2910387 AAACCCTCCT
*
2910397 CCAAATCCTCCTCCT-ATCCCA
1 CCAAATCCTACTCCTAATCCCA
*
2910418 CCAAATCCTATTCCTAATCCCA
1 CCAAATCCTACTCCTAATCCCA
2910440 TTGATCCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.28, C:0.47, G:0.00, T:0.26
Consensus pattern (22 bp):
CCAAATCCTACTCCTAATCCCA
Found at i:2913060 original size:31 final size:31
Alignment explanation
Indices: 2913047--2913272 Score: 116
Period size: 28 Copynumber: 7.8 Consensus size: 31
2913037 TATTAAATTT
*
2913047 TAACTTTAATGATTTGATAATAATTAATAGA
1 TAACTTTAATGATTTAATAATAATTAATAGA
* *
2913078 TAACTTTAATGATTTAATAATAATTAGTAGT
1 TAACTTTAATGATTTAATAATAATTAATAGA
* * * * *
2913109 TAAATTTAATAATTTGACTTTATGATT--T-GA
1 TAACTTTAATGATTT-A-ATAATAATTAATAGA
* * **
2913139 T-AC--TAATTA-TTAGTAACT--TTAATGATT
1 TAACTTTAATGATTTAATAA-TAATTAAT-AGA
* *
2913166 TAACTTTAAT-ATTT-A-AAT-A--AGTAGT
1 TAACTTTAATGATTTAATAATAATTAATAGA
*
2913191 TAACTTTAATGATTTAATAATAA-TAAT--T
1 TAACTTTAATGATTTAATAATAATTAATAGA
*
2913219 TAACTTTAATGATTTAATAATAA-TAAT--T
1 TAACTTTAATGATTTAATAATAATTAATAGA
*
2913247 TAACTTTAATTATTTAATAATAATTA
1 TAACTTTAATGATTTAATAATAATTA
2913273 TTTAATAATA
Statistics
Matches: 157, Mismatches: 20, Indels: 38
0.73 0.09 0.18
Matches are distributed among these distances:
23 2 0.01
24 2 0.01
25 15 0.10
26 8 0.05
27 8 0.05
28 58 0.37
29 5 0.03
30 10 0.06
31 42 0.27
32 1 0.01
33 6 0.04
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (31 bp):
TAACTTTAATGATTTAATAATAATTAATAGA
Found at i:2913134 original size:44 final size:44
Alignment explanation
Indices: 2913078--2913272 Score: 135
Period size: 39 Copynumber: 4.6 Consensus size: 44
2913068 AATTAATAGA
2913078 TAACTTTAATGATTTAATAATAATTAGTAGTTAAATTTAATAATT
1 TAACTTTAATGATTTAATAATAATTAGTAG-TAAATTTAATAATT
* * * * * *
2913123 TGACTTT-ATGATTTGATACTAATTATTAGTAACTTTAATGATT
1 TAACTTTAATGATTTAATAATAATTAGTAGTAAATTTAATAATT
* * *
2913166 TAACTTTAAT-ATTT-A-AATAAGTAGT--TAACTTTAATGATT
1 TAACTTTAATGATTTAATAATAATTAGTAGTAAATTTAATAATT
* * * *
2913205 TAA-TAATAATAATTTAACTTTAATGATT--TAAT-AA--TAATAATT
1 TAACT-TTAATGATTTAA---TAATAATTAGTAGTAAATTTAATAATT
*
2913247 TAACTTTAATTATTTAATAATAATTA
1 TAACTTTAATGATTTAATAATAATTA
2913273 TTTAATAATA
Statistics
Matches: 120, Mismatches: 18, Indels: 29
0.72 0.11 0.17
Matches are distributed among these distances:
38 1 0.01
39 28 0.23
40 4 0.03
41 8 0.07
42 21 0.17
43 24 0.20
44 22 0.18
45 12 0.10
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (44 bp):
TAACTTTAATGATTTAATAATAATTAGTAGTAAATTTAATAATT
Found at i:2913171 original size:14 final size:14
Alignment explanation
Indices: 2913152--2913263 Score: 92
Period size: 14 Copynumber: 8.2 Consensus size: 14
2913142 TAATTATTAG
2913152 TAACTTTAATGATT
1 TAACTTTAATGATT
2913166 TAACTTTAAT-ATT
1 TAACTTTAATGATT
* *
2913179 TAA--ATAA-GTAGT
1 TAACTTTAATG-ATT
2913191 TAACTTTAATGATT
1 TAACTTTAATGATT
* *
2913205 TAA-TAATAATAATT
1 TAACT-TTAATGATT
2913219 TAACTTTAATGATT
1 TAACTTTAATGATT
* *
2913233 TAA-TAATAATAATT
1 TAACT-TTAATGATT
*
2913247 TAACTTTAATTATT
1 TAACTTTAATGATT
2913261 TAA
1 TAA
2913264 TAATAATTAT
Statistics
Matches: 77, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
11 3 0.04
12 5 0.06
13 8 0.10
14 58 0.75
15 3 0.04
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (14 bp):
TAACTTTAATGATT
Found at i:2913221 original size:28 final size:28
Alignment explanation
Indices: 2913158--2913277 Score: 167
Period size: 28 Copynumber: 4.4 Consensus size: 28
2913148 TTAGTAACTT
*
2913158 TAATGATTTAACTTTAAT-ATTT-A-AA
1 TAATAATTTAACTTTAATGATTTAATAA
*
2913183 TAAGT-AGTTAACTTTAATGATTTAATAA
1 TAA-TAATTTAACTTTAATGATTTAATAA
2913211 TAATAATTTAACTTTAATGATTTAATAA
1 TAATAATTTAACTTTAATGATTTAATAA
*
2913239 TAATAATTTAACTTTAATTATTTAATAA
1 TAATAATTTAACTTTAATGATTTAATAA
*
2913267 TAATTATTTAA
1 TAATAATTTAA
2913278 TAATAGTAAT
Statistics
Matches: 86, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
25 15 0.17
26 5 0.06
27 2 0.02
28 64 0.74
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.47
Consensus pattern (28 bp):
TAATAATTTAACTTTAATGATTTAATAA
Found at i:2913270 original size:14 final size:14
Alignment explanation
Indices: 2913197--2913287 Score: 87
Period size: 14 Copynumber: 6.5 Consensus size: 14
2913187 TAGTTAACTT
*
2913197 TAATGATTTAATAA
1 TAATAATTTAATAA
*
2913211 TAATAATTTAACT-T
1 TAATAATTTAA-TAA
*
2913225 TAATGATTTAATAA
1 TAATAATTTAATAA
*
2913239 TAATAATTTAACT-T
1 TAATAATTTAA-TAA
*
2913253 TAATTATTTAATAA
1 TAATAATTTAATAA
*
2913267 TAATTATTTAATAA
1 TAATAATTTAATAA
*
2913281 TAGTAAT
1 TAATAAT
2913288 AATATTCGAT
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
13 2 0.03
14 59 0.94
15 2 0.03
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (14 bp):
TAATAATTTAATAA
Found at i:2915733 original size:172 final size:172
Alignment explanation
Indices: 2915386--2915734 Score: 637
Period size: 172 Copynumber: 2.0 Consensus size: 172
2915376 TAAAACGATT
2915386 CCTAATTACTATTTGGTTCTCAACATTTTCAAACTTTGTAATTTAATCCCTAAATTTATAAATTC
1 CCTAATTACTATTTGGTTCTCAACATTTTCAAACTTTGTAATTTAATCCCTAAATTTATAAATTC
*
2915451 TTTCAAATTTAACCAATTAAGCATACAATACTAAATTCCAGTATAGTATACCAACTTTTAATAAT
66 TTTCAAATTTAACCAATTAAGCATACAATACTAAATTCCAATATAGTATACCAACTTTTAATAAT
2915516 TTACTCTTATTCCTTAAATTCCTCAAATTTTACAAAATAATC
131 TTACTCTTATTCCTTAAATTCCTCAAATTTTACAAAATAATC
*
2915558 CCTAATTACTATTTGGTTCTCAATATTTTCAAACTTTGTAATTTAATCCCTAAATTTATAAATTC
1 CCTAATTACTATTTGGTTCTCAACATTTTCAAACTTTGTAATTTAATCCCTAAATTTATAAATTC
*
2915623 TTTCAAATTTAACCAATTTAGCATACTAATACTAAATTCCAATATAGTATACCAACTTTTAATAA
66 TTTCAAATTTAACCAATTAAGCATAC-AATACTAAATTCCAATATAGTATACCAACTTTTAATAA
* *
2915688 TTTACTCTTATTCCTTAAATTCCTCAAATTTTA-TAAATGATC
130 TTTACTCTTATTCCTTAAATTCCTCAAATTTTACAAAATAATC
2915730 CCTAA
1 CCTAA
2915735 ACTTTACAAT
Statistics
Matches: 171, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
172 101 0.59
173 70 0.41
ACGTcount: A:0.37, C:0.18, G:0.03, T:0.42
Consensus pattern (172 bp):
CCTAATTACTATTTGGTTCTCAACATTTTCAAACTTTGTAATTTAATCCCTAAATTTATAAATTC
TTTCAAATTTAACCAATTAAGCATACAATACTAAATTCCAATATAGTATACCAACTTTTAATAAT
TTACTCTTATTCCTTAAATTCCTCAAATTTTACAAAATAATC
Found at i:2916227 original size:23 final size:23
Alignment explanation
Indices: 2916197--2916305 Score: 145
Period size: 23 Copynumber: 4.9 Consensus size: 23
2916187 CAATTGCATG
2916197 ATACAGACGTGCAGGCCCCCCAC
1 ATACAGACGTGCAGGCCCCCCAC
*
2916220 ATACAGACGTGCAGGCCCCCTAC
1 ATACAGACGTGCAGGCCCCCCAC
*
2916243 ATACAGACGTGCAGGCCCCCTAC
1 ATACAGACGTGCAGGCCCCCCAC
* *
2916266 ATGC--ACGTACAGG-CCCCCAC
1 ATACAGACGTGCAGGCCCCCCAC
*
2916286 ATGCAGACGTGCA-GCCCCCC
1 ATACAGACGTGCAGGCCCCCC
2916306 TGCTTACCCG
Statistics
Matches: 78, Mismatches: 5, Indels: 7
0.87 0.06 0.08
Matches are distributed among these distances:
20 10 0.13
21 9 0.12
22 11 0.14
23 48 0.62
ACGTcount: A:0.25, C:0.42, G:0.22, T:0.11
Consensus pattern (23 bp):
ATACAGACGTGCAGGCCCCCCAC
Found at i:2916813 original size:60 final size:60
Alignment explanation
Indices: 2916749--2916908 Score: 223
Period size: 60 Copynumber: 2.7 Consensus size: 60
2916739 TTGGATGATA
* * *
2916749 CTTTGTAGAGTCCTTCGACTATTAAAAGTTATAAAATGGTCCCCTAATTATAAGATGTTG
1 CTTTGTTGAGTCCTTCGACTATTAAAAGTTATAAAATGGTCCCCCAACTATAAGATGTTG
* * * * *
2916809 CTTTGTTGAGTCCTTCGGCTATTAAAAGTTACAAAATGATCCCCCAACTATAGGGTGTTG
1 CTTTGTTGAGTCCTTCGACTATTAAAAGTTATAAAATGGTCCCCCAACTATAAGATGTTG
*
2916869 CTTTGTTGAGT-CTCCCGACTATTAAAAGTTATAAAATGGT
1 CTTTGTTGAGTCCT-TCGACTATTAAAAGTTATAAAATGGT
2916909 AACCCCCACT
Statistics
Matches: 87, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
59 2 0.02
60 85 0.98
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (60 bp):
CTTTGTTGAGTCCTTCGACTATTAAAAGTTATAAAATGGTCCCCCAACTATAAGATGTTG
Found at i:2944024 original size:20 final size:20
Alignment explanation
Indices: 2943980--2944240 Score: 159
Period size: 20 Copynumber: 12.6 Consensus size: 20
2943970 AATGACCAAT
*
2943980 AAAATCGCAACGCGATATA-
1 AAAATCGCAACGCGATTTAG
2943999 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
**
2944019 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
2944039 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
2944060 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
2944083 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
2944103 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
2944123 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* * *
2944143 AGAGTCGCAACGCGATCTAG
1 AAAATCGCAACGCGATTTAG
*
2944163 AAGAGAGTCGCAACGCGATCTAG
1 AA-A-A-TCGCAACGCGATTTAG
* * *
2944186 AAGAGAATCGCAATGCGACTGAG
1 -A-A-AATCGCAACGCGATTTAG
*
2944209 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
*
2944229 AGAATCGCAACG
1 AAAATCGCAACG
2944241 GTCAAAAGAA
Statistics
Matches: 192, Mismatches: 36, Indels: 27
0.75 0.14 0.11
Matches are distributed among these distances:
18 1 0.01
19 19 0.10
20 109 0.57
21 15 0.08
22 1 0.01
23 42 0.22
24 2 0.01
25 3 0.02
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:2944349 original size:12 final size:12
Alignment explanation
Indices: 2944340--2944430 Score: 126
Period size: 12 Copynumber: 8.2 Consensus size: 12
2944330 CATTACCATT
2944340 ACCACGACCACG
1 ACCACGACCACG
2944352 ACCACGACCACG
1 ACCACGACCACG
2944364 ACCACGACCACG
1 ACCACGACCACG
2944376 ACCACGACCACG
1 ACCACGACCACG
2944388 ACC-CGACC-CG
1 ACCACGACCACG
2944398 ACC-CGACC-CG
1 ACCACGACCACG
2944408 ACC-CGACC-CG
1 ACCACGACCACG
2944418 ACC-CGACC-CG
1 ACCACGACCACG
2944428 ACC
1 ACC
2944431 CGAGACGAGA
Statistics
Matches: 79, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
10 35 0.44
11 5 0.06
12 39 0.49
ACGTcount: A:0.27, C:0.55, G:0.18, T:0.00
Consensus pattern (12 bp):
ACCACGACCACG
Found at i:2944355 original size:18 final size:18
Alignment explanation
Indices: 2944340--2944430 Score: 126
Period size: 18 Copynumber: 5.5 Consensus size: 18
2944330 CATTACCATT
2944340 ACCACGACCACGACCACG
1 ACCACGACCACGACCACG
2944358 ACCACGACCACGACCACG
1 ACCACGACCACGACCACG
2944376 ACCACGACCACGACC-CG
1 ACCACGACCACGACCACG
2944393 ACC-CGACC-CGACC-CG
1 ACCACGACCACGACCACG
2944408 ACC-CGACC-CGACC-CG
1 ACCACGACCACGACCACG
2944423 ACC-CGACC
1 ACCACGACC
2944431 CGAGACGAGA
Statistics
Matches: 73, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
15 30 0.41
16 5 0.07
17 5 0.07
18 33 0.45
ACGTcount: A:0.27, C:0.55, G:0.18, T:0.00
Consensus pattern (18 bp):
ACCACGACCACGACCACG
Found at i:2944374 original size:30 final size:27
Alignment explanation
Indices: 2944344--2944430 Score: 133
Period size: 25 Copynumber: 3.2 Consensus size: 27
2944334 ACCATTACCA
2944344 CGACCACGACCACGACCACGACCACGACC
1 CGACCACGACCACGACC-CGACC-CGACC
2944373 ACGACCACGACCACGACCCGACCCGACC
1 -CGACCACGACCACGACCCGACCCGACC
2944401 CGACC-CGACC-CGACCCGACCCGACC
1 CGACCACGACCACGACCCGACCCGACC
2944426 CGACC
1 CGACC
2944431 CGAGACGAGA
Statistics
Matches: 57, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
25 20 0.35
26 5 0.09
27 5 0.09
28 5 0.09
29 5 0.09
30 17 0.30
ACGTcount: A:0.26, C:0.55, G:0.18, T:0.00
Consensus pattern (27 bp):
CGACCACGACCACGACCCGACCCGACC
Found at i:2944396 original size:5 final size:5
Alignment explanation
Indices: 2944344--2944433 Score: 117
Period size: 5 Copynumber: 16.6 Consensus size: 5
2944334 ACCATTACCA
2944344 CGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC CGACC
1 CGACC -CGACC -CGACC -CGACC -CGACC -CGACC -CGACC -CGACC CGACC
2944396 CGACC CGACC CGACC CGACC CGACC CGACC CGACC CGA
1 CGACC CGACC CGACC CGACC CGACC CGACC CGACC CGA
2944434 GACGAGACGG
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 43 0.51
6 41 0.49
ACGTcount: A:0.27, C:0.54, G:0.19, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:2945165 original size:6 final size:6
Alignment explanation
Indices: 2945119--2945288 Score: 291
Period size: 6 Copynumber: 29.5 Consensus size: 6
2945109 TCTCGTCTCG
2945119 GGTCG- GGTCG- GGTCG- GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2945160 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2945208 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2945256 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
2945289 AATACGTGTC
Statistics
Matches: 164, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 35 0.21
6 129 0.79
ACGTcount: A:0.00, C:0.17, G:0.52, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:2945390 original size:20 final size:20
Alignment explanation
Indices: 2945365--2945404 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2945355 TTTTTAACTA
*
2945365 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
2945385 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
2945405 CTCTCAGTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.17, G:0.17, T:0.53
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:2945420 original size:20 final size:20
Alignment explanation
Indices: 2945397--2945547 Score: 194
Period size: 20 Copynumber: 7.4 Consensus size: 20
2945387 CTTTTTAACG
2945397 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTCAGTCGCA
2945417 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTCAGTCGCA
2945437 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTCAGTCGCA
* *
2945457 TTGCGATTTTCTTCTAGATCGCG
1 TTGCGATTCTC-TC-AG-TCGCA
* *
2945480 TTGCGACTCTCTCAATCGCA
1 TTGCGATTCTCTCAGTCGCA
* * *
2945500 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTCAGTCGCA
* *
2945520 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTCTCAGTCGCA
2945540 TTGCGATT
1 TTGCGATT
2945548 TTCTTCTAAA
Statistics
Matches: 118, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
20 98 0.83
21 3 0.03
22 4 0.03
23 13 0.11
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.36
Consensus pattern (20 bp):
TTGCGATTCTCTCAGTCGCA
Found at i:2945421 original size:40 final size:41
Alignment explanation
Indices: 2945377--2945552 Score: 148
Period size: 40 Copynumber: 4.3 Consensus size: 41
2945367 CTTTTGACCG
* *
2945377 TTGCGATTTTCTTTTTAA-CGTTGCGATTCTCTCAGTCGCA
1 TTGCGATTTTCTTATTAATCGTTGCGATTCTCTCAATCGCA
* * * ** * *
2945417 TTGCGATTCTCTCAGT-CGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTTTCTTATTAATCGTTGCGATTCTCTCAATCGCA
* *
2945457 TTGCGATTTTCTT-CTAGATCGCGTTGCGACTCTCTCAATCGCA
1 TTGCGATTTTCTTATTA-AT--CGTTGCGATTCTCTCAATCGCA
* *
2945500 TTGCGA--TTC-TATAAATCGCATTGCGATTCTATCAATCGCA
1 TTGCGATTTTCTTATTAATCG--TTGCGATTCTCTCAATCGCA
2945540 TTGCGATTTTCTT
1 TTGCGATTTTCTT
2945553 CTAAATCGCG
Statistics
Matches: 107, Mismatches: 18, Indels: 19
0.74 0.12 0.13
Matches are distributed among these distances:
38 2 0.02
39 1 0.01
40 71 0.66
41 4 0.04
42 3 0.03
43 26 0.24
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TTGCGATTTTCTTATTAATCGTTGCGATTCTCTCAATCGCA
Found at i:2945491 original size:83 final size:83
Alignment explanation
Indices: 2945395--2945568 Score: 276
Period size: 83 Copynumber: 2.1 Consensus size: 83
2945385 TTCTTTTTAA
* * * * * * *
2945395 CGTTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCATTG
1 CGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTG
*
2945460 CGATTTTCTTCTAGATCG
66 CGATTTTCTTCTAAATCG
2945478 CGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTG
1 CGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTG
2945543 CGATTTTCTTCTAAATCG
66 CGATTTTCTTCTAAATCG
2945561 CGTTGCGA
1 CGTTGCGA
2945569 ACTTGGAAGC
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.18, C:0.26, G:0.19, T:0.36
Consensus pattern (83 bp):
CGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTG
CGATTTTCTTCTAAATCG
Found at i:2945499 original size:63 final size:60
Alignment explanation
Indices: 2945397--2945545 Score: 190
Period size: 63 Copynumber: 2.4 Consensus size: 60
2945387 CTTTTTAACG
* * * * *
2945397 TTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTCAGTCGCATTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCA
* *
2945457 TTGCGATTTTCTTCTAGATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCA
1 TTGCGATTCTC-TC-AG-TCGCATTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCA
* *
2945520 TTGCGATTCTATCAATCGCATTGCGA
1 TTGCGATTCTCTCAGTCGCATTGCGA
2945546 TTTTCTTCTA
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
60 20 0.27
61 3 0.04
62 4 0.05
63 48 0.64
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.36
Consensus pattern (60 bp):
TTGCGATTCTCTCAGTCGCATTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCA
Found at i:2945584 original size:21 final size:21
Alignment explanation
Indices: 2945558--2945610 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
2945548 TTCTTCTAAA
2945558 TCGCGTTGCGAACTTGGAAGC
1 TCGCGTTGCGAACTTGGAAGC
2945579 TCGCGTTGCGAACTTGGAAGC
1 TCGCGTTGCGAACTTGGAAGC
2945600 TCGCGTTGCGA
1 TCGCGTTGCGA
2945611 TTTTCTTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.17, C:0.25, G:0.34, T:0.25
Consensus pattern (21 bp):
TCGCGTTGCGAACTTGGAAGC
Found at i:2945703 original size:19 final size:20
Alignment explanation
Indices: 2945395--2945713 Score: 140
Period size: 20 Copynumber: 15.6 Consensus size: 20
2945385 TTCTTTTTAA
* * *
2945395 CGTTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
2945415 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
2945435 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* *
2945455 CATTGCGATTTTCTTCTAGATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
2945478 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
2945498 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
2945518 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
2945538 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
2945561 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
** ** *
2945582 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
2945603 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
2945621 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
2945643 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
2945663 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
2945683 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
2945702 CGTTGCGATTTT
1 CGTTGCGATTTT
2945714 ATTGGTCATT
Statistics
Matches: 249, Mismatches: 39, Indels: 23
0.80 0.13 0.07
Matches are distributed among these distances:
18 2 0.01
19 17 0.07
20 162 0.65
21 35 0.14
22 6 0.02
23 27 0.11
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:2953022 original size:23 final size:24
Alignment explanation
Indices: 2952992--2953040 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2952982 TTGGCCGTTT
2952992 AATTT-AA-AATTTTAGAGAAAATA
1 AATTTAAAGAATTTTAGA-AAAATA
*
2953015 AATTTAAAGAATTTTATAAAAATA
1 AATTTAAAGAATTTTAGAAAAATA
2953039 AA
1 AA
2953041 AATAAATTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 5 0.22
24 10 0.43
25 8 0.35
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (24 bp):
AATTTAAAGAATTTTAGAAAAATA
Found at i:2953046 original size:24 final size:25
Alignment explanation
Indices: 2952999--2953046 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
2952989 TTTAATTTAA
**
2952999 AATTTTAGAGAAAATAAATTTAAAG
1 AATTTTAGAGAAAATAAAAATAAAG
*
2953024 AATTTTATA-AAAATAAAAATAAA
1 AATTTTAGAGAAAATAAAAATAAA
2953047 TTACCTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (25 bp):
AATTTTAGAGAAAATAAAAATAAAG
Found at i:2955874 original size:13 final size:13
Alignment explanation
Indices: 2955858--2955882 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2955848 CATATAGTTT
2955858 ATCCAATTCTGTA
1 ATCCAATTCTGTA
2955871 ATCCAATTCTGT
1 ATCCAATTCTGT
2955883 CGAACCTACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.40
Consensus pattern (13 bp):
ATCCAATTCTGTA
Found at i:2956641 original size:117 final size:118
Alignment explanation
Indices: 2956492--2956730 Score: 376
Period size: 118 Copynumber: 2.0 Consensus size: 118
2956482 CAGTTAAGAT
*
2956492 AATTAAATTATAACTTTTTTAAAAGAGACTCATTATAACT-AAACCAATAA-TTTGTGGCATTTA
1 AATTAAATTATAACTTTTTTAAAAGAGACTCATTATAACTGAAA-CAATAATTTTGTGACATTTA
*
2956555 TTTATAATGAGTCTATATAAAATCTGATCCGAATTAATCAATTAATAGATTGAA
65 TTTATAATGAATCTATATAAAATCTGATCCGAATTAATCAATTAATAGATTGAA
* *
2956609 AATTAAATTATAAC-TTTTTAGGAAGAGACTCATTATAACTGAAACAATAATTTTGTGACATTTC
1 AATTAAATTATAACTTTTTTA-AAAGAGACTCATTATAACTGAAACAATAATTTTGTGACATTTA
* * *
2956673 TTTATAATGAATCTTTATAAAATCTGATTCGAATTAATCATTTAATAGATTGAA
65 TTTATAATGAATCTATATAAAATCTGATCCGAATTAATCAATTAATAGATTGAA
2956727 AATT
1 AATT
2956731 GAGGGCTATA
Statistics
Matches: 112, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
116 6 0.05
117 38 0.34
118 68 0.61
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.39
Consensus pattern (118 bp):
AATTAAATTATAACTTTTTTAAAAGAGACTCATTATAACTGAAACAATAATTTTGTGACATTTAT
TTATAATGAATCTATATAAAATCTGATCCGAATTAATCAATTAATAGATTGAA
Found at i:2958622 original size:104 final size:104
Alignment explanation
Indices: 2958443--2958651 Score: 391
Period size: 104 Copynumber: 2.0 Consensus size: 104
2958433 TCTCTCTTAC
*
2958443 ACACACACACATAGATACAACTAAAAGTCTAAAACAGACGCACACACATGTACCGCGTCTTTAGA
1 ACACACACACATAGATACAACTAAAAGTCTAAAACAGACGCACACACATGTACCACGTCTTTAGA
2958508 AAGATTAAGCAAACACTTTTTATGTTCCTCAGGAAACAT
66 AAGATTAAGCAAACACTTTTTATGTTCCTCAGGAAACAT
2958547 ACACACACACATAGATACAACTAAAAGTCTAAAACAGACGCACACACATGTACCACGTCTTTAGA
1 ACACACACACATAGATACAACTAAAAGTCTAAAACAGACGCACACACATGTACCACGTCTTTAGA
* *
2958612 AAGATTAAGCAAGCACTTTTTTTGTTCCTCAGGAAACAT
66 AAGATTAAGCAAACACTTTTTATGTTCCTCAGGAAACAT
2958651 A
1 A
2958652 TCTAGCTTCT
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 102 1.00
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.22
Consensus pattern (104 bp):
ACACACACACATAGATACAACTAAAAGTCTAAAACAGACGCACACACATGTACCACGTCTTTAGA
AAGATTAAGCAAACACTTTTTATGTTCCTCAGGAAACAT
Found at i:2969211 original size:21 final size:22
Alignment explanation
Indices: 2969165--2969211 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
2969155 TTAGGTTTCT
*
2969165 TTGTTTAGGCAATCTTTTGTAA
1 TTGTTTAGGCAATCTTATGTAA
*
2969187 -TGTTT-GGTAATCTTATGTAA
1 TTGTTTAGGCAATCTTATGTAA
2969207 TTGTT
1 TTGTT
2969212 GGCTATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.21, C:0.06, G:0.19, T:0.53
Consensus pattern (22 bp):
TTGTTTAGGCAATCTTATGTAA
Found at i:2969533 original size:78 final size:78
Alignment explanation
Indices: 2969382--2969533 Score: 252
Period size: 78 Copynumber: 1.9 Consensus size: 78
2969372 CAATTTATAA
* * *
2969382 ATAATGAAAAGTTTGTAGCAATCTATCTGGCTTATGTTCTTTGTTCATTGTTTTGAAGGGTTACT
1 ATAATGAAAAATTTGTAGCAATATATCTGGCTTATATTCTTTGTTCATTGTTTTGAAGGGTTACT
*
2969447 GTGGGGCTGCTAT
66 GTGAGGCTGCTAT
2969460 ATAATGAAAAATTTGTAGCAATATATCTGGCTTATATTCTTTGTTCATTGTTTTGAAGGGTTACC
1 ATAATGAAAAATTTGTAGCAATATATCTGGCTTATATTCTTTGTTCATTGTTTTGAAGGGTTA-C
2969525 T-TGAGGCTG
65 TGTGAGGCTG
2969534 AGATATTACC
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
78 67 0.97
79 2 0.03
ACGTcount: A:0.24, C:0.11, G:0.22, T:0.42
Consensus pattern (78 bp):
ATAATGAAAAATTTGTAGCAATATATCTGGCTTATATTCTTTGTTCATTGTTTTGAAGGGTTACT
GTGAGGCTGCTAT
Found at i:2977489 original size:6 final size:6
Alignment explanation
Indices: 2977478--2977506 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2977468 CTAAACCCTA
2977478 AACCCG AACCCG AACCCG AACCCG AACCC
1 AACCCG AACCCG AACCCG AACCCG AACCC
2977507 AATTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.52, G:0.14, T:0.00
Consensus pattern (6 bp):
AACCCG
Found at i:2985738 original size:51 final size:51
Alignment explanation
Indices: 2985661--2985761 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
2985651 CCTTCCTCTG
* * * **
2985661 TGGATTCTAATGGACCCGCATTCTATTTTACTTTGTACATGTATTTTACTC
1 TGGATTCTAATGGACCCACATACTATTTAACTTTGTACATAAATTTTACTC
*
2985712 TGGATTCTAATGGACCCATATACTATTTAACTTTGTACATAAATTTTACT
1 TGGATTCTAATGGACCCACATACTATTTAACTTTGTACATAAATTTTACT
2985762 TTTTTTATAG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.44
Consensus pattern (51 bp):
TGGATTCTAATGGACCCACATACTATTTAACTTTGTACATAAATTTTACTC
Found at i:2994064 original size:20 final size:20
Alignment explanation
Indices: 2994039--2994079 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2994029 AGGTGTAATT
2994039 TACCCGTATTTATATTACTA
1 TACCCGTATTTATATTACTA
2994059 TACCCGTATTTATATTACTA
1 TACCCGTATTTATATTACTA
2994079 T
1 T
2994080 TCTTTTGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.46
Consensus pattern (20 bp):
TACCCGTATTTATATTACTA
Found at i:2999637 original size:131 final size:131
Alignment explanation
Indices: 2999436--2999672 Score: 318
Period size: 131 Copynumber: 1.8 Consensus size: 131
2999426 ATAATTCTAA
* * * * *
2999436 GAGAGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACATTTCATGCCTTAAAACG
1 GAGAGAAAACGACAATATCAAATTATTTCCAATCGAGAATAAATGACATCTCATACCTTAAAACG
* * * *
2999501 ATCATTTATTACTCCA-ATCGGAATGAAGAGATATTACTATTTCGTCTTAAAATTCAATATTAAT
66 ATCATTTATCACT-CAGACCGAAATGAAAAGATATTACTATTTCGTCTTAAAATTCAATATTAAT
2999565 TC
130 TC
* *
2999567 GAGAGAAAACGACAATATCAAATTATTTCCAATTGAGAATAAATGATC-TCTCATACCTTAAAGC
1 GAGAGAAAACGACAATATCAAATTATTTCCAATCGAGAATAAATGA-CATCTCATACCTTAAAAC
*
2999631 -AGTCATTTATCACTTAGACCGAAATGAAAAGATATTACTATT
65 GA-TCATTTATCACTCAGACCGAAATGAAAAGATATTACTATT
2999673 CTCAATATCG
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
130 2 0.02
131 88 0.97
132 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (131 bp):
GAGAGAAAACGACAATATCAAATTATTTCCAATCGAGAATAAATGACATCTCATACCTTAAAACG
ATCATTTATCACTCAGACCGAAATGAAAAGATATTACTATTTCGTCTTAAAATTCAATATTAATT
C
Found at i:3000336 original size:29 final size:28
Alignment explanation
Indices: 3000263--3000336 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 28
3000253 TTACAAAGAA
* *
3000263 TAAAAATAAATAAAACATGAGGACTAAAT
1 TAAAAATAAATAAAA-ATGACGACCAAAT
*
3000292 TAAAAATAAACTAAAATTGCACGACCAAAT
1 TAAAAATAAA-TAAAAATG-ACGACCAAAT
3000322 T-AAAATAAATAAAAA
1 TAAAAATAAATAAAAA
3000337 GATAAATTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
28 5 0.13
29 20 0.51
30 14 0.36
ACGTcount: A:0.64, C:0.09, G:0.07, T:0.20
Consensus pattern (28 bp):
TAAAAATAAATAAAAATGACGACCAAAT
Found at i:3001904 original size:3 final size:3
Alignment explanation
Indices: 3001896--3001928 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3001886 ATTGGCACAC
3001896 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3001929 GTGGTTCTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3002431 original size:134 final size:133
Alignment explanation
Indices: 3002111--3002943 Score: 1030
Period size: 134 Copynumber: 6.2 Consensus size: 133
3002101 CGTCGACTCG
* * *
3002111 TTCCACTGTT-CTTCAGGGAATATTAAATCGAGGTAGACTTGTTCCA-TAGTTACTTAGGGAATA
1 TTCCACTGTTAC-TCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACT-GTTACTCAGGGAATA
* * * * * * * **
3002174 TTAAATGC-TGAAAGAGGGGGATCTGTTTCGCTTTTTCTTGAGGGAAAATCAGATAT-AGGACCT
64 TCAAAT-CTTGAAAGAGAGGGATTTGTTCCGCTTTTTC-CGAGGGAAAATCAGATCTGGGGATGT
3002237 TGATTCA
127 TGATTCA
* * * * *
3002244 TTCCATTGTTAGTCAGGGAAGATTGAATCGAGGCAGACTTATTCCACTGTTACTCAGGGAATATT
1 TTCCACTGTTACTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAATATC
3002309 AAATCTTGAAAGAGAGGGATTTGTTCCGCTTCTTTCCGAGGGAAAATCAGATCTGGGGATGTTGA
66 AAATCTTGAAAGAGAGGGATTTGTTCCGCTT-TTTCCGAGGGAAAATCAGATCTGGGGATGTTGA
*
3002374 TTTA
130 TTCA
* * **
3002378 TTCCACTGTTACTCAGGGAAGATTGAATCGAGGCAGACTTGTTCCACTATTACTCAAAGAATATC
1 TTCCACTGTTACTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAATATC
* * **
3002443 AAATCTTGAAAGAGAGGGATCTT-TTCCGCTTCTTCCTGAGGGAAAATCAAATCTGGGGACATTG
66 AAATCTTGAAAGAGAGGGAT-TTGTTCCGCTTTTTCC-GAGGGAAAATCAGATCTGGGGATGTTG
3002507 ATTCA
129 ATTCA
* * * * *
3002512 TACCACTGTTACTTAGGGAAGATTGAATCGAGGTAGACTAGTTCCATTTTTACTCAGGGAATATC
1 TTCCACTGTTACTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAATATC
* * * * *
3002577 AAATCTTGAAAAAGAGAGATTTATTCCGCTTTTTCCTGAGGAAAAATCAGATTTGGGGATGTTGA
66 AAATCTTGAAAGAGAGGGATTTGTTCCGCTTTTTCC-GAGGGAAAATCAGATCTGGGGATGTTGA
*
3002642 TTAA
130 TTCA
* * *
3002646 TTACACTGTTTCTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAACATC
1 TTCCACTGTTACTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAATATC
* * *
3002711 AAATCTTGAAAGAGAGGGATATGTTCCGCTTCTTCTTGAGGGAAAATCAGATCTGGGGATGTTGA
66 AAATCTTGAAAGAGAGGGATTTGTTCCGCTTTTTC-CGAGGGAAAATCAGATCTGGGGATGTTGA
3002776 TTCA
130 TTCA
* * * * *
3002780 TTCCACTATCACCCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGTTATTCAGGGAATATC
1 TTCCACTGTTACTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAATATC
* * * ** * * *
3002845 AAATCTTGAAAGAGAAGGATTTGTTTCACTTTTTTTGAGGGAAAATTAGATC-CGGGATATTGAT
66 AAATCTTGAAAGAGAGGGATTTGTTCCGCTTTTTCCGAGGGAAAATCAGATCTGGGGATGTTGAT
3002909 TCA
131 TCA
*
3002912 TTCCACTGTCACTCAGGGAAGATTGAATCGAG
1 TTCCACTGTTACTCAGGGAAGATTGAATCGAG
3002944 TTCGATTCGT
Statistics
Matches: 610, Mismatches: 81, Indels: 19
0.86 0.11 0.03
Matches are distributed among these distances:
132 44 0.07
133 119 0.20
134 445 0.73
135 2 0.00
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (133 bp):
TTCCACTGTTACTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTCAGGGAATATC
AAATCTTGAAAGAGAGGGATTTGTTCCGCTTTTTCCGAGGGAAAATCAGATCTGGGGATGTTGAT
TCA
Found at i:3003315 original size:21 final size:22
Alignment explanation
Indices: 3003263--3003324 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 22
3003253 CATGTGAGAA
*
3003263 CATCCTGCTCGAAGGACTTATG
1 CATCTTGCTCGAAGGACTTATG
* *
3003285 GA--TGGCTCGAAGGACTTAT-
1 CATCTTGCTCGAAGGACTTATG
3003304 CATCTTGCTCGAGAGG-CTTAT
1 CATCTTGCTCGA-AGGACTTAT
3003325 AGATGACCCG
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
19 1 0.03
20 15 0.47
21 12 0.38
22 4 0.12
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.29
Consensus pattern (22 bp):
CATCTTGCTCGAAGGACTTATG
Found at i:3003377 original size:42 final size:41
Alignment explanation
Indices: 3003263--3003468 Score: 175
Period size: 41 Copynumber: 5.0 Consensus size: 41
3003253 CATGTGAGAA
* * * * *
3003263 CATCCTGCTCGAAGGACTTATGGATGGCTCGAAGGACTTAT
1 CATCATGCTCGAAAGACTTATAGATGGCCCGAAGGACTTAG
* * * * *
3003304 CATCTTGCTCGAGAGGCTTATAGATGACCCGAAGGATTTAAG
1 CATCATGCTCGAAAGACTTATAGATGGCCCGAAGGACTT-AG
*
3003346 CATCATGCTCGAAAGACTTACT-GATGGCCCGAAGGACTTAT
1 CATCATGCTCGAAAGACTTA-TAGATGGCCCGAAGGACTTAG
* * * * *
3003387 CATCTTGCTC-AAGAGGCTTATAGATGACCCAAAGGATTTAAG
1 CATCATGCTCGAA-AGACTTATAGATGGCCCGAAGGACTT-AG
* * *
3003429 CATCATGCTTGAAAGACTTACT-GATGGCCTGAAAGACTTA
1 CATCATGCTCGAAAGACTTA-TAGATGGCCCGAAGGACTTA
3003469 CCAAATTTGA
Statistics
Matches: 129, Mismatches: 29, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
40 3 0.02
41 62 0.48
42 60 0.47
43 4 0.03
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (41 bp):
CATCATGCTCGAAAGACTTATAGATGGCCCGAAGGACTTAG
Found at i:3003407 original size:83 final size:83
Alignment explanation
Indices: 3003263--3003468 Score: 324
Period size: 83 Copynumber: 2.5 Consensus size: 83
3003253 CATGTGAGAA
* * * *
3003263 CATCCTGCTCGAAGGACTTA-TGGATGGCTCGAAGGACTTATCATCTTGCTCGAGAGGCTTATAG
1 CATCATGCTCGAAAGACTTACT-GATGGCCCGAAGGACTTATCATCTTGCTCAAGAGGCTTATAG
*
3003327 ATGACCCGAAGGATTTAAG
65 ATGACCCAAAGGATTTAAG
3003346 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATCATCTTGCTCAAGAGGCTTATAGA
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATCATCTTGCTCAAGAGGCTTATAGA
3003411 TGACCCAAAGGATTTAAG
66 TGACCCAAAGGATTTAAG
* * *
3003429 CATCATGCTTGAAAGACTTACTGATGGCCTGAAAGACTTA
1 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA
3003469 CCAAATTTGA
Statistics
Matches: 114, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
83 113 0.99
84 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (83 bp):
CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATCATCTTGCTCAAGAGGCTTATAGA
TGACCCAAAGGATTTAAG
Found at i:3003679 original size:41 final size:41
Alignment explanation
Indices: 3003604--3003704 Score: 123
Period size: 41 Copynumber: 2.5 Consensus size: 41
3003594 ATGTATTATG
* *
3003604 GATGACCCGAAGGACTTATCATCTTTCTCAAAAGAC-TACA
1 GATGACCCGAAGGACTTATCATCATGCTCAAAAGACTTACA
** * *
3003644 GATGACCCGAAGGGTTTAATCATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGACTT-ATCATCATGCTCAAAAGACTTACA
*
3003686 GATGCCCCGAAGGACTTAT
1 GATGACCCGAAGGACTTAT
3003705 AAATTTTGGA
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
40 15 0.30
41 18 0.36
42 17 0.34
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.25
Consensus pattern (41 bp):
GATGACCCGAAGGACTTATCATCATGCTCAAAAGACTTACA
Found at i:3005369 original size:3 final size:3
Alignment explanation
Indices: 3005361--3005424 Score: 83
Period size: 3 Copynumber: 21.3 Consensus size: 3
3005351 TGCATTAAAA
* * * * *
3005361 AAT AAT AAT ATT AAT AAT ACT AAT AAT AGT AGT AGT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3005409 AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT A
3005425 GTCTGGACGA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:3010004 original size:58 final size:59
Alignment explanation
Indices: 3009934--3010054 Score: 208
Period size: 58 Copynumber: 2.1 Consensus size: 59
3009924 TCTTCTTTCA
*
3009934 CCTTGTGCGCTCTCGAAATGCCAGTCGAACTTGGCA-TTTTTATTTAACTCAACAATCT
1 CCTTGTGCGCTCTCGAAATACCAGTCGAACTTGGCATTTTTTATTTAACTCAACAATCT
**
3009992 CCTTGTGCGCTCTCGAAATACCAGTCGAACTTGGCATTTTTTATTTAACTCAGTAATCT
1 CCTTGTGCGCTCTCGAAATACCAGTCGAACTTGGCATTTTTTATTTAACTCAACAATCT
3010051 CCTT
1 CCTT
3010055 ATGTCGTGGT
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
58 35 0.59
59 24 0.41
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (59 bp):
CCTTGTGCGCTCTCGAAATACCAGTCGAACTTGGCATTTTTTATTTAACTCAACAATCT
Found at i:3023852 original size:22 final size:22
Alignment explanation
Indices: 3023805--3023863 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
3023795 TATAGAAATT
* * *
3023805 ATTTATTAGAAATATGAATATT
1 ATTTATTATAAATATTAATATA
3023827 ATTTATTATAAATATTAA-AGTA
1 ATTTATTATAAATATTAATA-TA
3023849 ATTTATT-T-AATATTA
1 ATTTATTATAAATATTA
3023864 TTTGTTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 7 0.21
21 2 0.06
22 24 0.73
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (22 bp):
ATTTATTATAAATATTAATATA
Done.