Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001444.1 Hibiscus syriacus cultivar Beakdansim tig00002793_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: 2564052
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 12
Found at i:2453396 original size:21 final size:20
Alignment explanation
Indices: 2453368--2453425 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
2453358 GAAGGTATAA
*
2453368 ATTTTATT-TTATTTTTTATT
1 ATTTTATTAATATTTTTT-TT
2453388 ATATTTATTGAATATTTTTTTT
1 AT-TTTATT-AATATTTTTTTT
2453410 ATTTTATTAATTATTT
1 ATTTTATTAA-TATTT
2453426 GTAATTAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
20 4 0.12
21 17 0.52
22 4 0.12
23 8 0.24
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (20 bp):
ATTTTATTAATATTTTTTTT
Found at i:2455911 original size:169 final size:167
Alignment explanation
Indices: 2455618--2456130 Score: 668
Period size: 169 Copynumber: 3.0 Consensus size: 167
2455608 TTCCCCCCAA
* *
2455618 TGGGAACATGATATCTGCATATAATTGACTGAAATATGCATAGATAATCTGACAAAAAAGGAAGA
1 TGGGAACATGATATATGCATATAATTGACTGAAATATGCATAGATAATCTGACAAAAAGGGAAG-
* * * *
2455683 CTTGTTCCACAAGAAG-CACTTTCGCCTTTTTCAAAGAATATTTGTTATGTCATAATGTCTCATC
65 CTCGTTCCACAAGAAGTGA-TTTCGCCTTTTTCAAAGAAT-CTTGTCATGTCATAATGTCTCATC
*
2455747 CCATCAAACATATATGGGGTTGACGTGAATAGTACCATGAC
128 CCATCAAACATATATGGGGTTGATGTGAATAGT-CCATGAC
* * ** *
2455788 TGGGAACATGATATATGCATATAATTGAATGATATATAAAGAGATAATCTGACAAAAAGGGAAGC
1 TGGGAACATGATATATGCATATAATTGACTGAAATATGCATAGATAATCTGACAAAAAGGGAAGC
* * * * * * *
2455853 TCGTTCCACAAAAAGTGTTTTCACCTTTTTTAAAGAATCTCTATCATGTCATAATGTCTCGTCCT
66 TCGTTCCACAAGAAGTGATTTCGCCTTTTTCAAAGAATCT-TGTCATGTCATAATGTCTCATCCC
* ** *
2455918 ATCAAACATATATGGGGTTGATGTAAATAGTGCCACAAT
130 ATCAAACATATATGGGGTTGATGTGAATAGT-CCATGAC
*
2455957 TTGGAACATGATATATGCATATAATTGACTGAAATATGCATAGATAATCTGACAAAAAGGGAAGG
1 TGGGAACATGATATATGCATATAATTGACTGAAATATGCATAGATAATCTGACAAAAAGGGAA-G
* * * *
2456022 CTCATTCCACAAGAAGTGATTTCGCCTTTTTCAAATAATCATTGTCATGCCATAATATCTCATCC
65 CTCGTTCCACAAGAAGTGATTTCGCCTTTTTCAAAGAATC-TTGTCATGTCATAATGTCTCATCC
* * *
2456087 CATCAAACATAAATGGGGTTAATGTGAATAGTTCATGAC
129 CATCAAACATATATGGGGTTGATGTGAATAGTCCATGAC
2456126 TGGGA
1 TGGGA
2456131 TCATCATGTC
Statistics
Matches: 290, Mismatches: 49, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
168 1 0.00
169 149 0.51
170 139 0.48
171 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (167 bp):
TGGGAACATGATATATGCATATAATTGACTGAAATATGCATAGATAATCTGACAAAAAGGGAAGC
TCGTTCCACAAGAAGTGATTTCGCCTTTTTCAAAGAATCTTGTCATGTCATAATGTCTCATCCCA
TCAAACATATATGGGGTTGATGTGAATAGTCCATGAC
Found at i:2458184 original size:18 final size:18
Alignment explanation
Indices: 2458141--2458177 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2458131 TGAGATCAAA
*
2458141 GTACCATTGGACTCTTTG
1 GTACCAATGGACTCTTTG
2458159 GTACCAATGGACTCTTTG
1 GTACCAATGGACTCTTTG
2458177 G
1 G
2458178 GTCCAATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.22, G:0.24, T:0.35
Consensus pattern (18 bp):
GTACCAATGGACTCTTTG
Found at i:2462206 original size:2 final size:2
Alignment explanation
Indices: 2462199--2462233 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2462189 TTGAAAATGA
2462199 AT AT 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 AT AT A
2462234 CATCAAAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2462500 original size:10 final size:10
Alignment explanation
Indices: 2462465--2462507 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
2462455 TAAGATTTAA
2462465 AAAATAATAAT
1 AAAATAAT-AT
* *
2462476 ATAATGAATAA
1 AAAAT-AATAT
2462487 AAAATAATAT
1 AAAATAATAT
2462497 AAAATAATAT
1 AAAATAATAT
2462507 A
1 A
2462508 TATATATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 15 0.56
11 9 0.33
12 3 0.11
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (10 bp):
AAAATAATAT
Found at i:2462551 original size:25 final size:23
Alignment explanation
Indices: 2462498--2462551 Score: 54
Period size: 25 Copynumber: 2.3 Consensus size: 23
2462488 AAATAATATA
* *
2462498 AAATAATATATATATATATAAAG
1 AAATAAGATATATATAAATAAAG
**
2462521 TTATAAGATATATACGTAAATAAAG
1 AAATAAGATATATA--TAAATAAAG
2462546 AAATAA
1 AAATAA
2462552 TAAATAAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
23 11 0.48
25 12 0.52
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.31
Consensus pattern (23 bp):
AAATAAGATATATATAAATAAAG
Found at i:2462704 original size:2 final size:2
Alignment explanation
Indices: 2462697--2462721 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2462687 TATTAAAGAA
2462697 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 A
2462722 ATAAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2462812 original size:17 final size:18
Alignment explanation
Indices: 2462779--2462814 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2462769 ATATATACAT
*
2462779 ATAATAATAACATGAATA
1 ATAAAAATAACATGAATA
2462797 ATAAAAATAA-ATGAATA
1 ATAAAAATAACATGAATA
2462814 A
1 A
2462815 AATATCCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (18 bp):
ATAAAAATAACATGAATA
Found at i:2466054 original size:39 final size:39
Alignment explanation
Indices: 2465957--2466055 Score: 191
Period size: 38 Copynumber: 2.6 Consensus size: 39
2465947 ATGACAGAGA
2465957 ATAAGGGAGTATGTAATAGTATTAACAAAGAATAAAGGT
1 ATAAGGGAGTATGTAATAGTATTAACAAAGAATAAAGGT
2465996 ATAA-GGAGTATGTAATAGTATTAACAAAGAATAAAGGT
1 ATAAGGGAGTATGTAATAGTATTAACAAAGAATAAAGGT
2466034 ATAAGGGAGTATGTAATAGTAT
1 ATAAGGGAGTATGTAATAGTAT
2466056 ATAAGATTAG
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
38 38 0.64
39 21 0.36
ACGTcount: A:0.47, C:0.02, G:0.23, T:0.27
Consensus pattern (39 bp):
ATAAGGGAGTATGTAATAGTATTAACAAAGAATAAAGGT
Found at i:2469729 original size:210 final size:209
Alignment explanation
Indices: 2469359--2469778 Score: 621
Period size: 210 Copynumber: 2.0 Consensus size: 209
2469349 CTTTAGAAGT
*
2469359 GAGAAAGTAAACAAGGTGAGATGAATTGTTGTAAAGATAAAATAAAATATATTATTTTAATCAAT
1 GAGAAAGTAAAAAAGGTGAGATGAATTGTTGTAAAGATAAAATAAAATATATTATTTTAATCAAT
* * *
2469424 ATTTTTTAATTTAAAAATTTAGAATAAAATGTTGACATTAGTTTCTTACCTACGTCAAAGAGCAC
66 ATTTTTTAATTTAAAAATTTAAAATAAAAGGTTGACATTAGTTTCTTACCTACGTCAAAAAGCAC
* *
2469489 AAAGCTCAAGAAATAGGTGTGCAGAATTTTTAACTCTTAATATAATATATTAAATATTGACA-GT
131 AAAGCTCAAGAAATAGGTATGCAGAATTTTTAACTCTTAATAAAATATATTAAATATTGACATGT
2469553 TTTAAGGAAAATGG
196 TTTAAGGAAAATGG
* * *
2469567 GAGAAAGTAAAAAAGGTGAGATGAATTGTTGTAAAAGGTAAAATAATATATATTATTTTAATCAG
1 GAGAAAGTAAAAAAGGTGAGATGAATTGTTGT-AAAGATAAAATAAAATATATTATTTTAATCAA
* * *
2469632 TATTTTTTTAATTTAAAATTTTAAAATAAAAGGTTGATATTA-TCTTTTTA-CTCACGTCAAAAA
65 TA-TTTTTTAATTTAAAAATTTAAAATAAAAGGTTGACATTAGT-TTCTTACCT-ACGTCAAAAA
* * * *
2469695 GTACAAAGCTCAAGAAATAGGTATGCATAATTTTTAACTCTTAATAAAATATATTAAATGTTGAT
127 GCACAAAGCTCAAGAAATAGGTATGCAGAATTTTTAACTCTTAATAAAATATATTAAATATTGAC
*
2469760 ATTTTTTTAAGGAAAATGG
192 A-TGTTTTAAGGAAAATGG
2469779 ATATGCATTT
Statistics
Matches: 189, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
208 31 0.16
209 34 0.18
210 109 0.58
212 15 0.08
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (209 bp):
GAGAAAGTAAAAAAGGTGAGATGAATTGTTGTAAAGATAAAATAAAATATATTATTTTAATCAAT
ATTTTTTAATTTAAAAATTTAAAATAAAAGGTTGACATTAGTTTCTTACCTACGTCAAAAAGCAC
AAAGCTCAAGAAATAGGTATGCAGAATTTTTAACTCTTAATAAAATATATTAAATATTGACATGT
TTTAAGGAAAATGG
Found at i:2471059 original size:41 final size:41
Alignment explanation
Indices: 2470964--2471302 Score: 407
Period size: 41 Copynumber: 8.3 Consensus size: 41
2470954 AGACTCGTGA
* * * * * *
2470964 TTTAGTGGCGTTTATATAAAAACGGCGATAAAGAATGA-AC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATAC
*
2471004 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATAT
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATAC
* *
2471045 TTTAGTGGCATTTTTATACAAACGCCGCTAAAGACTCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATAC
* * * *
2471086 TTTAGTGGTGTTTTTATAAAAACGCCGCTATAGACTCGTAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATAC
* * *
2471127 TTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCGTGC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATAC
* * *
2471168 TTTAGTGGCGTTTTTATATAAACGCCGCTAACGACTCGTTA-
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTC-ATAC
*
2471209 TTTAGTGGTGTTTTTATACAAACG-CGCTAAAGACTCATAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATAC
* * * *
2471249 TTTTGTAGCGTTTTTATACAAACACCACTAACA-ACTCATAC
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAA-AGACTCATAC
*
2471290 TTTAGTGGAGTTT
1 TTTAGTGGCGTTT
2471303 GTGTTTACAA
Statistics
Matches: 260, Mismatches: 34, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
39 2 0.01
40 63 0.24
41 193 0.74
42 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (41 bp):
TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATAC
Found at i:2471156 original size:123 final size:121
Alignment explanation
Indices: 2470954--2471297 Score: 449
Period size: 123 Copynumber: 2.8 Consensus size: 121
2470944 AACTCGTACT
* * * * *
2470954 AGACTCGTGATTTAGTGGCGTTTATATAAAAACGGCGATAAAGAAT-GAACTTTAGTGGCGTTTT
1 AGACTCGT-ATTTAGTGGTGTTTTTATAAAAAC-GCGCTAAAGACTCGTACTTTAGTGGCGTTTT
*
2471018 TATACAAACGCCGCTAAAGACTCATATTTTAGTGGCATTTTTATACAAACGCCGCTAA
64 TATACAAACGCCGCTAAAGACTCATACTTTAGTGGCATTTTTATACAAACGCCGCTAA
*
2471076 AGACTCGTACTTTAGTGGTGTTTTTATAAAAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTT
1 AGACTCGTA-TTTAGTGGTGTTTTTATAAAAACG-CGCTAAAGACTCGTACTTTAGTGGCGTTTT
* * * * *
2471141 TATACAAACGCCGCTATAGACTCGTGCTTTAGTGGCGTTTTTATATAAACGCCGCTAA
64 TATACAAACGCCGCTAAAGACTCATACTTTAGTGGCATTTTTATACAAACGCCGCTAA
* * * * *
2471199 CGACTCGTTATTTAGTGGTGTTTTTATACAAACGCGCTAAAGACTCATACTTTTGTAGCGTTTTT
1 AGACTCG-TATTTAGTGGTGTTTTTATAAAAACGCGCTAAAGACTCGTACTTTAGTGGCGTTTTT
* *
2471264 ATACAAACACCACTAACA-ACTCATACTTTAGTGG
65 ATACAAACGCCGCTAA-AGACTCATACTTTAGTGG
2471298 AGTTTGTGTT
Statistics
Matches: 194, Mismatches: 23, Indels: 10
0.85 0.10 0.04
Matches are distributed among these distances:
121 2 0.01
122 91 0.47
123 99 0.51
124 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (121 bp):
AGACTCGTATTTAGTGGTGTTTTTATAAAAACGCGCTAAAGACTCGTACTTTAGTGGCGTTTTTA
TACAAACGCCGCTAAAGACTCATACTTTAGTGGCATTTTTATACAAACGCCGCTAA
Found at i:2471569 original size:21 final size:22
Alignment explanation
Indices: 2471540--2471580 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2471530 ATATTAAATG
*
2471540 TTATTAAATA-TCTTTAAATAA
1 TTATCAAATATTCTTTAAATAA
*
2471561 TTATCAAATATTTTTTAAAT
1 TTATCAAATATTCTTTAAAT
2471581 TAATCAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (22 bp):
TTATCAAATATTCTTTAAATAA
Found at i:2471615 original size:20 final size:20
Alignment explanation
Indices: 2471586--2471631 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 20
2471576 TAAATTAATC
2471586 AATTTATTATTAATGATTATTAA
1 AATTTATTA--AATGATTA-TAA
*
2471609 AATTTATTAAATTATTATAA
1 AATTTATTAAATGATTATAA
2471629 AAT
1 AAT
2471632 AAACTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 7 0.32
23 9 0.41
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
AATTTATTAAATGATTATAA
Found at i:2471640 original size:62 final size:62
Alignment explanation
Indices: 2471531--2471649 Score: 143
Period size: 62 Copynumber: 1.9 Consensus size: 62
2471521 TTGTAAAGTA
* ***
2471531 TATTAAATGTTATTAAATATCTTTAAATAATTATCAAATATTTTTTAAATTAATCAATTTAT
1 TATTAAATGTTATTAAATATCTTTAAATAATTATAAAATAAACTTTAAATTAATCAATTTAT
* * *
2471593 TATT-AATGATTATTAAA-ATTTATTAAATTATTATAAAATAAACTTTAAATTTATCAA
1 TATTAAATG-TTATTAAATATCT-TTAAATAATTATAAAATAAACTTTAAATTAATCAA
2471650 AATATTATAC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
61 7 0.15
62 41 0.85
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (62 bp):
TATTAAATGTTATTAAATATCTTTAAATAATTATAAAATAAACTTTAAATTAATCAATTTAT
Found at i:2471959 original size:19 final size:19
Alignment explanation
Indices: 2471943--2472196 Score: 157
Period size: 21 Copynumber: 12.3 Consensus size: 19
2471933 AATGCGATTT
2471943 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
* *
2471962 TCCAAGTTCGCGTTGCGATTTAT
1 TCCAAATT--CGTTGCGA--TAG
2471985 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
*
2472004 TCCAAGTTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
* * *
2472023 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAATT--CGTTGCGA--TAG
2472046 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
* * * *
2472065 TCGAAGTTCGCGTTGGGATTTAT
1 TCCAAATT--CGTTGCGA--TAG
*
2472088 TCCAAGTTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
* * *
2472107 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAATT--CGTTGCGA--TAG
* *
2472130 TCCAAGTTCGTTGTGATAG
1 TCCAAATTCGTTGCGATAG
* * *
2472149 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAATT--CGTTGCGA--TAG
2472172 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
2472191 TCCAAA
1 TCCAAA
2472197 ATCGCAACGA
Statistics
Matches: 187, Mismatches: 28, Indels: 40
0.73 0.11 0.16
Matches are distributed among these distances:
19 68 0.36
21 76 0.41
23 43 0.23
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (19 bp):
TCCAAATTCGTTGCGATAG
Found at i:2472014 original size:61 final size:61
Alignment explanation
Indices: 2471943--2472195 Score: 307
Period size: 61 Copynumber: 4.1 Consensus size: 61
2471933 AATGCGATTT
*
2471943 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
*
2472004 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
* * * * * *
2472065 TCGAAGTTCGCGTTGGGATTTATTCCAAGTT--CGTTGCGA--TAGTCGAAGTTCGCGTTGCGAT
1 TCCAAGTT--CGTTGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT--CGTTGCGA-
*
2472126 TTAT
59 -TAG
* *
2472130 TCCAAGTTCGTTGTGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
2472191 TCCAA
1 TCCAA
2472196 AATCGCAACG
Statistics
Matches: 162, Mismatches: 18, Indels: 24
0.79 0.09 0.12
Matches are distributed among these distances:
61 90 0.56
63 46 0.28
65 26 0.16
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.35
Consensus pattern (61 bp):
TCCAAGTTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
Found at i:2472050 original size:42 final size:42
Alignment explanation
Indices: 2472004--2472192 Score: 342
Period size: 42 Copynumber: 4.5 Consensus size: 42
2471994 GTTGCGATAG
2472004 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
* *
2472046 TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGGGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
2472088 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
*
2472130 TCCAAGTTCGTTGTGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
*
2472172 TCCAAATTCGTTGCGATAGTC
1 TCCAAGTTCGTTGCGATAGTC
2472193 CAAAATCGCA
Statistics
Matches: 140, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 140 1.00
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (42 bp):
TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
Found at i:2472062 original size:103 final size:102
Alignment explanation
Indices: 2471935--2472125 Score: 312
Period size: 103 Copynumber: 1.9 Consensus size: 102
2471925 ACTATCGCAA
2471935 TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCG
1 TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCG
2472000 ATAGTCCAAGTT-CGTTGCGATAGTCGAAGTTCGCGT
66 ATAGTCCAAGTTCCGTTGCGATAGTCGAAGTTCGCGT
* * *
2472036 TGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGGGATTTATTCCAAGTTCGTTG
1 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTG
*
2472101 CGATAGTCGAAGTTCGCGTTGCGAT
64 CGATAGTCCAAGTTC-CGTTGCGAT
2472126 TTATTCCAAG
Statistics
Matches: 82, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
101 5 0.06
102 2 0.02
103 66 0.80
105 9 0.11
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.35
Consensus pattern (102 bp):
TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCG
ATAGTCCAAGTTCCGTTGCGATAGTCGAAGTTCGCGT
Found at i:2473104 original size:21 final size:21
Alignment explanation
Indices: 2473080--2473128 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
2473070 TTTGAAATAA
2473080 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
2473101 ATCGCAA--CGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
*
2473120 ACCGCAACG
1 ATCGCAACG
2473129 AATTGTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 17 0.71
21 7 0.29
ACGTcount: A:0.31, C:0.33, G:0.20, T:0.16
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:2473460 original size:66 final size:66
Alignment explanation
Indices: 2473354--2473485 Score: 237
Period size: 66 Copynumber: 2.0 Consensus size: 66
2473344 AAAATGCCTC
*
2473354 AGTGTTACCCACAGCAACATCATCAATTGTGAACATCCGACGTGACAAACTTAATTAGCAACCGT
1 AGTGTTACCCACAGCAACATCATCAAGTGTGAACATCCGACGTGACAAACTTAATTAGCAACCGT
2473419 T
66 T
* *
2473420 AGTGTTACCCACGGCAACATCATCAAGTGTGAACATCCGACGTGGCAAACTTAATTAGCAACCGT
1 AGTGTTACCCACAGCAACATCATCAAGTGTGAACATCCGACGTGACAAACTTAATTAGCAACCGT
2473485 T
66 T
2473486 GGATCAAGGA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.23
Consensus pattern (66 bp):
AGTGTTACCCACAGCAACATCATCAAGTGTGAACATCCGACGTGACAAACTTAATTAGCAACCGT
T
Found at i:2476747 original size:43 final size:43
Alignment explanation
Indices: 2476681--2476855 Score: 197
Period size: 43 Copynumber: 4.1 Consensus size: 43
2476671 TACACTATCA
** * * *
2476681 TTGTAAAGACAAGTGTCGTTAAATACATAATCAATAGCGGTGT
1 TTGTAAAGACAAACGTCGCTAAATACACAATCAATAGCGGCGT
* * * * *
2476724 TTCTAAAGAAAAATGTCGCTAAATATACAGTCAATAGCGGCGT
1 TTGTAAAGACAAACGTCGCTAAATACACAATCAATAGCGGCGT
* * * * *
2476767 TTGTAAATACAAACGTCACTAAATACACAATCAATAGTGACAT
1 TTGTAAAGACAAACGTCGCTAAATACACAATCAATAGCGGCGT
* *
2476810 TTGTAAAGACAAACGTCGCTAAATATACAGTCAATAGCGGCGT
1 TTGTAAAGACAAACGTCGCTAAATACACAATCAATAGCGGCGT
2476853 TTG
1 TTG
2476856 CCGCTAAATA
Statistics
Matches: 107, Mismatches: 25, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 107 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (43 bp):
TTGTAAAGACAAACGTCGCTAAATACACAATCAATAGCGGCGT
Found at i:2476864 original size:31 final size:31
Alignment explanation
Indices: 2476826--2476886 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
2476816 AGACAAACGT
* *
2476826 CGCTAAATATACAGTCAATAGCGGCGTTTGC
1 CGCTAAATACACAGTCAATAGCGGCATTTGC
2476857 CGCTAAATACACAGTCAATAGCGGCATTTG
1 CGCTAAATACACAGTCAATAGCGGCATTTG
2476887 TAAATAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (31 bp):
CGCTAAATACACAGTCAATAGCGGCATTTGC
Found at i:2476891 original size:27 final size:29
Alignment explanation
Indices: 2476825--2476892 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 29
2476815 AAGACAAACG
* *
2476825 TCGCTAAATATACAGTCAATAGCGGCGTT
1 TCGCTAAATACACAGTCAATAGCGGCATT
2476854 TGCCGCTAAATACACAGTCAATAGCGGCATT
1 T--CGCTAAATACACAGTCAATAGCGGCATT
2476885 T-G-TAAATA
1 TCGCTAAATA
2476893 AAAACGCTGC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
27 6 0.17
28 1 0.03
29 1 0.03
31 27 0.77
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (29 bp):
TCGCTAAATACACAGTCAATAGCGGCATT
Found at i:2483880 original size:19 final size:19
Alignment explanation
Indices: 2483856--2483895 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
2483846 TTTAAACGGG
2483856 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
2483875 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
2483894 TG
1 TG
2483896 TAGTGCATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.30, G:0.17, T:0.33
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:2483902 original size:24 final size:20
Alignment explanation
Indices: 2483855--2483912 Score: 73
Period size: 19 Copynumber: 2.8 Consensus size: 20
2483845 TTTTAAACGG
2483855 GTGCATCGATGCACTCCTTA
1 GTGCATCGATGCACTCCTTA
2483875 -TGCATCGATGCACTCCTTATGTA
1 GTGCATCGATGCACTCC---T-TA
2483898 GTGCATCGATGCACT
1 GTGCATCGATGCACT
2483913 ATTGGCATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 16 0.48
22 1 0.03
23 2 0.06
24 14 0.42
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.31
Consensus pattern (20 bp):
GTGCATCGATGCACTCCTTA
Found at i:2487327 original size:23 final size:23
Alignment explanation
Indices: 2487307--2487351 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
2487297 ACCTAAGTTC
2487307 CACGTAGAATTGCACCGAAGTGT
1 CACGTAGAATTGCACCGAAGTGT
*
2487330 CGCGTAGAATTGCACCGAAGTG
1 CACGTAGAATTGCACCGAAGTG
2487352 CCATATAAAA
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:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (23 bp):
CACGTAGAATTGCACCGAAGTGT
Found at i:2489912 original size:65 final size:65
Alignment explanation
Indices: 2489822--2489955 Score: 207
Period size: 65 Copynumber: 2.1 Consensus size: 65
2489812 ACACTAATTA
2489822 CATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATAG-TATGTGCATCGGTACACAAAAG
1 CATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATAGCT-TGTGCATCGGTACACAAAAG
2489886 G
65 G
* ** * *
2489887 CATTCGATGTTTCAAAATATTCAAGAGTGCATCGATGCATGGCTTGTGCATCGGTACACAAAATG
1 CATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATAGCTTGTGCATCGGTACACAAAAGG
2489952 CATT
1 CATT
2489956 TGAAATGGGT
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
65 62 0.98
66 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (65 bp):
CATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATAGCTTGTGCATCGGTACACAAAAGG
Found at i:2500196 original size:65 final size:65
Alignment explanation
Indices: 2500102--2500258 Score: 174
Period size: 65 Copynumber: 2.4 Consensus size: 65
2500092 TACACTAGGG
** * * *
2500102 GTGCATCGGTACATTAATTACATTTGATGTTTCAAAAGAGCC-AGAAGTGCATCAATGCATGG-T
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAGAGCCAAG-AGTGCATCAATGCATGGCT
2500165 CT
65 -T
* ** *
2500167 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAATATTCAAGAGTGCATCGATGCATGGCTT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAGAGCCAAGAGTGCATCAATGCATGGCTT
* * *
2500232 ATGCATCGGTACTCAAAATGTATTCGA
1 GTGCATCGGTACACAAAATGCATTCGA
2500259 AATGGGTGTG
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
65 75 0.96
66 3 0.04
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (65 bp):
GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAGAGCCAAGAGTGCATCAATGCATGGCTT
Found at i:2502884 original size:22 final size:23
Alignment explanation
Indices: 2502854--2502896 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
2502844 TTATAATAAT
2502854 TTTATTTTTATGACATGTTTTTC
1 TTTATTTTTATGACATGTTTTTC
*
2502877 TTTATTTTT-TGATATGTTTT
1 TTTATTTTTATGACATGTTTT
2502897 CATTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.16, C:0.05, G:0.09, T:0.70
Consensus pattern (23 bp):
TTTATTTTTATGACATGTTTTTC
Found at i:2504169 original size:20 final size:21
Alignment explanation
Indices: 2504134--2504172 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2504124 ATTAAAGCAG
2504134 ACTAAAACTAATAATTTAGAC
1 ACTAAAACTAATAATTTAGAC
*
2504155 ACTAAAAGT-ATAATTTAG
1 ACTAAAACTAATAATTTAG
2504173 CCAAATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.51, C:0.10, G:0.08, T:0.31
Consensus pattern (21 bp):
ACTAAAACTAATAATTTAGAC
Found at i:2506917 original size:20 final size:20
Alignment explanation
Indices: 2506892--2506932 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
2506882 TTATTGTGTT
2506892 TATTTATATT-CGTTCGTTTA
1 TATTTAT-TTACGTTCGTTTA
2506912 TATTTATTTACGTTCGTTTA
1 TATTTATTTACGTTCGTTTA
2506932 T
1 T
2506933 TTATTTTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.61
Consensus pattern (20 bp):
TATTTATTTACGTTCGTTTA
Found at i:2506935 original size:24 final size:24
Alignment explanation
Indices: 2506890--2506936 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
2506880 ATTTATTGTG
* *
2506890 TTTATTTATATTCGTTCGTTTATA
1 TTTATTTACATTCGTTCATTTATA
* *
2506914 TTTATTTACGTTCGTTTATTTAT
1 TTTATTTACATTCGTTCATTTAT
2506937 TTTTCAGATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.19, C:0.09, G:0.09, T:0.64
Consensus pattern (24 bp):
TTTATTTACATTCGTTCATTTATA
Found at i:2509329 original size:19 final size:20
Alignment explanation
Indices: 2509305--2509355 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
2509295 AATGACCAAT
2509305 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
2509324 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
2509344 AAAATCGCAACG
1 AAAATCGCAACG
2509356 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:2509349 original size:20 final size:20
Alignment explanation
Indices: 2509305--2509602 Score: 134
Period size: 20 Copynumber: 14.6 Consensus size: 20
2509295 AATGACCAAT
* *
2509305 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
2509324 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
2509344 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
2509364 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
** * **
2509384 AAAATCATAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
2509405 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * * *
2509428 AAAATCACAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
2509448 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
2509468 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
2509488 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
2509511 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
2509531 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
2509551 AGAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* ***
2509571 AAAATCGCAACGCTAAAAAG
1 AAAATCGCAACGCGATTTAG
2509591 AAAATCGCAACG
1 AAAATCGCAACG
2509603 GTCAAAAGAA
Statistics
Matches: 217, Mismatches: 50, Indels: 23
0.75 0.17 0.08
Matches are distributed among these distances:
19 17 0.08
20 160 0.74
21 12 0.06
23 28 0.13
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:2509507 original size:83 final size:83
Alignment explanation
Indices: 2509409--2509583 Score: 278
Period size: 83 Copynumber: 2.1 Consensus size: 83
2509399 GCTTCCAAGT
* * * *
2509409 TCGCAACGCGATTTAGAAGAAAATCACAATGCGATTGATAGAATCGCAATGCGATTTATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCACAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATC
* * *
2509474 GCAATGCGATTGAGAGAG
66 GCAACGCGATTGAGAAAA
*
2509492 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCACAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATC
2509557 GCAACGCGATTGAGAAAA
66 GCAACGCGATTGAGAAAA
2509575 TCGCAACGC
1 TCGCAACGC
2509584 TAAAAAGAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 84 1.00
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.19
Consensus pattern (83 bp):
TCGCAACGCGATTTAGAAGAAAATCACAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAATC
GCAACGCGATTGAGAAAA
Found at i:2509517 original size:63 final size:60
Alignment explanation
Indices: 2509430--2509580 Score: 203
Period size: 63 Copynumber: 2.5 Consensus size: 60
2509420 TTTAGAAGAA
* * * * * * *
2509430 AATCACAATGCGATTGATAGAATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAG
1 AATCGCAACGCGATTGAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAG
*
2509490 AGTCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAG
1 AATCGCAACGCGA-TT-G-AGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAG
2509553 AATCGCAACGCGATTGAGAAAATCGCAA
1 AATCGCAACGCGATTGAGAAAATCGCAA
2509581 CGCTAAAAAG
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
60 22 0.28
61 3 0.04
62 3 0.04
63 51 0.65
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (60 bp):
AATCGCAACGCGATTGAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAG
Found at i:2509609 original size:20 final size:20
Alignment explanation
Indices: 2509569--2509612 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2509559 AACGCGATTG
2509569 AGAAAATCGCAACGCTAAAA
1 AGAAAATCGCAACGCTAAAA
* *
2509589 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGCTAAAA
2509609 AGAA
1 AGAA
2509613 TAGTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.18, G:0.18, T:0.09
Consensus pattern (20 bp):
AGAAAATCGCAACGCTAAAA
Found at i:2509700 original size:6 final size:6
Alignment explanation
Indices: 2509689--2509791 Score: 176
Period size: 6 Copynumber: 17.7 Consensus size: 6
2509679 AGACACGTAT
*
2509689 GACCAC GACCAC GACCAC GACCAC GACCAT GACCAC GACCAC GACCAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
2509737 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC-C GACC-C
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
2509783 GACC-C GACC
1 GACCAC GACC
2509792 CGAGACGAGA
Statistics
Matches: 95, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
5 15 0.16
6 80 0.84
ACGTcount: A:0.31, C:0.50, G:0.17, T:0.01
Consensus pattern (6 bp):
GACCAC
Found at i:2510288 original size:6 final size:6
Alignment explanation
Indices: 2510229--2510287 Score: 91
Period size: 6 Copynumber: 9.8 Consensus size: 6
2510219 GGGTCGGGGT
* *
2510229 CGTGGC CGTGGC CGTGGC CGTGGC CGTGGC CGTGGC CGTGGT CGTGGT
1 CGTGGC CGTGGC CGTGGC CGTGGC CGTGGC CGTGGC CGTGGC CGTGGC
*
2510277 CGTGGT CGTGG
1 CGTGGC CGTGG
2510288 TAATACGTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.00, C:0.27, G:0.51, T:0.22
Consensus pattern (6 bp):
CGTGGC
Found at i:2510392 original size:20 final size:20
Alignment explanation
Indices: 2510367--2510406 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2510357 TTTTTAACTA
*
2510367 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
2510387 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
2510407 CTCTCAATCG
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:2510422 original size:20 final size:20
Alignment explanation
Indices: 2510399--2510549 Score: 185
Period size: 20 Copynumber: 7.4 Consensus size: 20
2510389 CTTTTTAACG
2510399 TTGCGATTCTCTCAATCGCA
1 TTGCGATTCTCTCAATCGCA
* *
2510419 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTCAATCGCA
*
2510439 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTCAATCGCA
* *
2510459 TTGCGATTTTCTTCTAAATCGCG
1 TTGCGA--TTC-TCTCAATCGCA
*
2510482 TTGCGACTCTCTCAATCGCA
1 TTGCGATTCTCTCAATCGCA
* *
2510502 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTCAATCGCA
*
2510522 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTCTCAATCGCA
*
2510542 TTGTGATT
1 TTGCGATT
2510550 TTCTTCTAAA
Statistics
Matches: 112, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
20 93 0.83
21 2 0.02
22 3 0.03
23 14 0.12
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.37
Consensus pattern (20 bp):
TTGCGATTCTCTCAATCGCA
Found at i:2510423 original size:40 final size:42
Alignment explanation
Indices: 2510379--2510562 Score: 204
Period size: 40 Copynumber: 4.5 Consensus size: 42
2510369 CTTTTGACCG
* *
2510379 TTGCGATTTTCTTTTTAA-CG-TTGCGATTCTCTCAATCGCA
1 TTGCGATTTTCTTATAAATCGATTGCGATTCTCTCAATCGCA
*
2510419 TTGCGA--TTC-TATAAATCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTTTCTTATAAATCG-ATTGCGATTCTCTCAATCGCA
* * *
2510459 TTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCA
1 TTGCGATTTTCTTATAAATCG-ATTGCGATTCTCTCAATCGCA
*
2510502 TTGCGA--TTC-TATAAATCGCATTGCGATTCTATCAATCGCA
1 TTGCGATTTTCTTATAAATCG-ATTGCGATTCTCTCAATCGCA
* *
2510542 TTGTGATTTTCTTCTAAATCG
1 TTGCGATTTTCTTATAAATCG
2510563 CGTTGCGAAC
Statistics
Matches: 122, Mismatches: 13, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
37 4 0.03
38 5 0.04
40 63 0.52
41 3 0.02
42 6 0.05
43 41 0.34
ACGTcount: A:0.21, C:0.23, G:0.16, T:0.40
Consensus pattern (42 bp):
TTGCGATTTTCTTATAAATCGATTGCGATTCTCTCAATCGCA
Found at i:2510515 original size:83 final size:83
Alignment explanation
Indices: 2510397--2510570 Score: 312
Period size: 83 Copynumber: 2.1 Consensus size: 83
2510387 TTCTTTTTAA
* * *
2510397 CGTTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCATTG
1 CGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTG
2510462 CGATTTTCTTCTAAATCG
66 CGATTTTCTTCTAAATCG
2510480 CGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTG
1 CGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTG
*
2510545 TGATTTTCTTCTAAATCG
66 CGATTTTCTTCTAAATCG
2510563 CGTTGCGA
1 CGTTGCGA
2510571 ACTTGGAAGC
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 87 1.00
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (83 bp):
CGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTG
CGATTTTCTTCTAAATCG
Found at i:2510562 original size:63 final size:59
Alignment explanation
Indices: 2510399--2510570 Score: 182
Period size: 63 Copynumber: 2.8 Consensus size: 59
2510389 CTTTTTAACG
* * * *
2510399 TTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTCT-TCAATCGCATTGCGATTCTCTAAATCGCATTGCGATTCTATAAATCGCA
* * *
2510459 TTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCA
1 TTGCGA--TTCTTC--AATCGCATTGCGATTCTCTAAATCGCATTGCGATTCTATAAATCGCA
* *
2510522 TTGCGATTCTATCAATCGCATTGTGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGATTCT-TCAATCGCATTGCGA--TTC-TCTAAATCGCATTGCGA
2510571 ACTTGGAAGC
Statistics
Matches: 92, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
60 17 0.18
61 6 0.07
62 8 0.09
63 61 0.66
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (59 bp):
TTGCGATTCTTCAATCGCATTGCGATTCTCTAAATCGCATTGCGATTCTATAAATCGCA
Found at i:2510613 original size:20 final size:20
Alignment explanation
Indices: 2510590--2510637 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
2510580 CTCGCGTTAT
*
2510590 GATTTTCTTTTGACCGTTGC
1 GATTTTCTTTTGAACGTTGC
*
2510610 GATTTTCTTTTTAACGTTGC
1 GATTTTCTTTTGAACGTTGC
2510630 GATTTTCT
1 GATTTTCT
2510638 AAATCGCGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.12, C:0.17, G:0.17, T:0.54
Consensus pattern (20 bp):
GATTTTCTTTTGAACGTTGC
Found at i:2510664 original size:19 final size:20
Alignment explanation
Indices: 2510624--2510674 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
2510614 TTCTTTTTAA
*
2510624 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
2510644 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
2510663 CGTTGCGATTTT
1 CGTTGCGATTTT
2510675 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:2511490 original size:21 final size:19
Alignment explanation
Indices: 2511457--2511497 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
2511447 AAAATATAGG
2511457 ATAAATATAAAATAGATAA
1 ATAAATATAAAATAGATAA
*
2511476 ATAAATGAGTAAAATATATAA
1 ATAAAT-A-TAAAATAGATAA
2511497 A
1 A
2511498 AAGTAAAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 1 0.05
21 12 0.63
ACGTcount: A:0.66, C:0.00, G:0.07, T:0.27
Consensus pattern (19 bp):
ATAAATATAAAATAGATAA
Found at i:2512107 original size:34 final size:34
Alignment explanation
Indices: 2512064--2512129 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
2512054 GAATCCTAGC
*
2512064 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGGTTGAATCCT
* *
2512098 AAAATTCTATCCTATTTTTAGGAGGTTGAATC
1 AAAATTCTATCATATCTTTAGGAGGTTGAATC
2512130 TTAGTAGGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (34 bp):
AAAATTCTATCATATCTTTAGGAGGTTGAATCCT
Found at i:2512894 original size:98 final size:98
Alignment explanation
Indices: 2512678--2512989 Score: 304
Period size: 98 Copynumber: 3.0 Consensus size: 98
2512668 CATTGTTCCA
2512678 AGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGAAAAATTGTTTGTTGACAA
1 AGTCCAATATCCTCCGCT-GTGAAGTTGAAATTGG--CT----CCG--AAATTGTTTGTTGACAA
* * *
2512742 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
57 CCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCG
* * * **
2512784 AGTCCAATATCCTTCGTTGTGAAGTTGAGATTGGCTCCGAAATTGTTTGTTGACAGTCAGCCGCC
1 AGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGCTCCGAAATTGTTTGTTGACAACCAGCCGCC
* *
2512849 CCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTG
66 CCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCG
* * *
2512882 GGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGC-CCTGAAACTGGGAAATTATTATTGACAAC
1 AGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGCTCC-GAAA-T-TG----T-TTGTTGACAAC
* * * *
2512946 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTG
58 CAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCG
2512987 AGT
1 AGT
2512990 GGCACGATAT
Statistics
Matches: 175, Mismatches: 22, Indels: 19
0.81 0.10 0.09
Matches are distributed among these distances:
97 2 0.01
98 87 0.50
99 1 0.01
100 4 0.02
104 3 0.02
105 47 0.27
106 30 0.17
107 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (98 bp):
AGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGCTCCGAAATTGTTTGTTGACAACCAGCCGCC
CCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCG
Found at i:2513715 original size:31 final size:31
Alignment explanation
Indices: 2513680--2513807 Score: 82
Period size: 31 Copynumber: 3.9 Consensus size: 31
2513670 GGGAAATAAA
2513680 CTCAAA-GATTTTGTGTTTCAAGAGAAACTGT
1 CTCAAACGATTTTGTGTTTCAAGAGAAACT-T
** * *
2513711 CTCAAGGGAGACGAAATT-TGTTTCAAGGGAAACAAT
1 CTC-A---A-ACGATTTTGTGTTTCAAGAGAAAC-TT
*
2513747 CTCAAA-GGTTTTGTGTTTCAAGAGAAACATT
1 CTCAAACGATTTTGTGTTTCAAGAGAAAC-TT
* * *
2513778 TTCAAAGGTTTTTTGTGTTTCAAGAGAAAC
1 CTCAAACG-ATTTTGTGTTTCAAGAGAAAC
2513808 AATTTCAAAG
Statistics
Matches: 76, Mismatches: 11, Indels: 18
0.72 0.10 0.17
Matches are distributed among these distances:
30 3 0.04
31 25 0.33
32 3 0.04
33 20 0.26
35 2 0.03
36 19 0.25
37 4 0.05
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (31 bp):
CTCAAACGATTTTGTGTTTCAAGAGAAACTT
Found at i:2513764 original size:67 final size:67
Alignment explanation
Indices: 2513582--2513774 Score: 233
Period size: 67 Copynumber: 2.8 Consensus size: 67
2513572 GTCTTAAAAA
* * * * ** *
2513582 AGACATAATTCGTTTCAAGGGAAACGATCTTAAAGATAAATGTTGTTTCATGAGAAACGGCCTCA
1 AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGAT-TTTG-TGTTTCAAGAGAAACGGCCTCA
2513647 AGGG
64 AGGG
* * * * *
2513651 AGACAAAATTTTGTTTTAAGGGAAATAAACTCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAA
1 AGACAAAA-TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACGGCCTCAA
2513716 GGG
65 GGG
* *
2513719 AGACGAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTTTGTGTTTCAAGAGAAAC
1 AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAAC
2513775 ATTTTCAAAG
Statistics
Matches: 106, Mismatches: 17, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
67 44 0.42
68 30 0.28
69 9 0.08
70 23 0.22
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.28
Consensus pattern (67 bp):
AGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACGGCCTCAAG
GG
Found at i:2513834 original size:36 final size:33
Alignment explanation
Indices: 2513729--2513843 Score: 162
Period size: 33 Copynumber: 3.5 Consensus size: 33
2513719 AGACGAAATT
* *
2513729 TGTTTCAAGGGAAACAATCTCAAAGG--TTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
*
2513760 TGTTTCAAGAGAAACATTTTCAAAGGTTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
2513793 TGTTTCAAGAGAAACAATTTCAAAGGTTTCTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGG--T-TTTTTG
2513829 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
2513844 TGTATCAAGG
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
31 23 0.31
33 30 0.40
35 1 0.01
36 21 0.28
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.37
Consensus pattern (33 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTG
Found at i:2513994 original size:36 final size:36
Alignment explanation
Indices: 2513885--2514407 Score: 188
Period size: 37 Copynumber: 15.4 Consensus size: 36
2513875 CAAGGATTGA
*
2513885 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * *
2513922 TGTTTTAAGAAAAACATGTCTTAAGAGAGACAAAATT
1 TGTTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAATT
* *
2513959 TGTTTCAAGAGAAACCGTCTCAAGAGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
2513995 TGTTT-AATGTA-AAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAA-G-AGAAAC-TGTCTCAAGAGAGACAAAATT
* * *
2514024 TGTTTCAAGGGAAACTGTTTTC-A-A-AG-----TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATT
*
2514053 ATGTTTCAATAGAAACTGTCTCAA-AGGAGACAAAATT
1 -TGTTTCAAGAGAAACTGTCTCAAGA-GAGACAAAATT
* *
2514090 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
** * * * *
2514126 CATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATT
* *
2514154 ATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* *
2514192 TGTTTCAAGGGAAACTATCTCAAGAGAGAC--AATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * * *
2514226 TATTTCAAGGGAAA-TGCTTTC-A-A-TG-----TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATT
*
2514254 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * *
2514292 TGTTCCAAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATT
*
2514320 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* *
2514358 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
** *
2514394 CATTTCAAGGGAAA
1 TGTTTCAAGAGAAA
2514408 TGTTTTCATG
Statistics
Matches: 366, Mismatches: 66, Indels: 109
0.68 0.12 0.20
Matches are distributed among these distances:
28 7 0.02
29 64 0.17
30 34 0.09
31 1 0.00
32 6 0.02
33 5 0.01
34 21 0.06
35 7 0.02
36 93 0.25
37 105 0.29
38 23 0.06
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:2514049 original size:30 final size:30
Alignment explanation
Indices: 2514013--2514071 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
2514003 GTAAAACATA
*
2514013 TTCAAAGATTT-TGTTTCAAGGGAAACTGTT
1 TTCAAAG-TTTATGTTTCAAGAGAAACTGTT
*
2514043 TTCAAAGTTTATGTTTCAATAGAAACTGT
1 TTCAAAGTTTATGTTTCAAGAGAAACTGT
2514072 CTCAAAGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (30 bp):
TTCAAAGTTTATGTTTCAAGAGAAACTGTT
Found at i:2514261 original size:100 final size:101
Alignment explanation
Indices: 2514026--2514305 Score: 465
Period size: 100 Copynumber: 2.8 Consensus size: 101
2514016 AAAGATTTTG
* * *
2514026 TTTCAAGGGAAACTGTTTTCAAAGTTTATGTTTCAATAGAAACTGTCTCAAAGGAGACAAAA-TT
1 TTTCAAGGGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
2514090 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
65 TGTTTCAAGGGAAACTATCTCAAGAGAGAC-AAATTCA
*
2514128 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
*
2514193 GTTTCAAGGGAAACTATCTCAAGAGAGAC-AATTTA
66 GTTTCAAGGGAAACTATCTCAAGAGAGACAAATTCA
*
2514228 TTTCAAGGGAAATGCTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
*
2514293 GTTCCAAGGGAAA
66 GTTTCAAGGGAAA
2514306 TGTTTTCAAT
Statistics
Matches: 169, Mismatches: 8, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
100 80 0.47
101 45 0.27
102 44 0.26
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (101 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
GTTTCAAGGGAAACTATCTCAAGAGAGACAAATTCA
Found at i:2514323 original size:166 final size:165
Alignment explanation
Indices: 2514090--2514473 Score: 594
Period size: 166 Copynumber: 2.3 Consensus size: 165
2514080 AGACAAAATT
* * *
2514090 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCAT-TTCAAGGGAAATGTTTTCAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT-TTGTTCAAGGGAAATGTTTTCAATGTTT
*
2514154 ATGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
65 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
*
2514219 GAC-AATTTATTTCAAGGGAAATGCTTTCAATGTTTA
130 GACAAATTCATTTCAAGGGAAATGCTTTC-ATGTTTA
*
2514255 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTCCAAGGGAAATGTTTTCAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTT-CAAGGGAAATGTTTTCAATGTTT
2514320 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
65 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGA
*
2514385 GACAAAATTCATTTCAAGGGAAATGTTTTCATGTTTA
130 GAC-AAATTCATTTCAAGGGAAATGCTTTCATGTTTA
* * *
2514422 TGTTTAAAGAG-AACTGTCTCAAGTGAGACAAAACTTTCTGTTTCGAGGGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTT-TG-TTCAAGGGAAA
2514474 CTATCTCAAG
Statistics
Matches: 202, Mismatches: 10, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
164 1 0.00
165 35 0.17
166 111 0.55
167 20 0.10
168 33 0.16
169 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (165 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTCAAGGGAAATGTTTTCAATGTTTA
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
ACAAATTCATTTCAAGGGAAATGCTTTCATGTTTA
Found at i:2514326 original size:66 final size:65
Alignment explanation
Indices: 2514192--2514371 Score: 276
Period size: 66 Copynumber: 2.8 Consensus size: 65
2514182 GACAAAATTT
* * *
2514192 TGTTTCAAGGGAAACTATCTCAAGAGAGAC--AATTTAT-TTCAAGGGAAATGCTTTCAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT-TGTTCAAGGGAAATGCTTTCAATGTTT
2514254 A
65 A
*
2514255 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTCCAAGGGAAATGTTTTCAATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTT-CAAGGGAAATGCTTTCAATGTTT
2514320 A
65 A
2514321 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTG-TTCAAGGGAAA
2514372 CTATCTCAAG
Statistics
Matches: 108, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
63 27 0.25
64 1 0.01
65 7 0.06
66 71 0.66
67 2 0.02
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTCAAGGGAAATGCTTTCAATGTTTA
Found at i:2514471 original size:102 final size:103
Alignment explanation
Indices: 2514255--2514494 Score: 344
Period size: 102 Copynumber: 2.3 Consensus size: 103
2514245 TCAATGTTTA
* * * *
2514255 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTCCAAGGGAAATGTTTTCAATGTTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTATGTTCCAAGGGAAATGTTTTCAATGTTT
*
2514320 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 ATGTTTAAAGAGAAACTGTCTCAAGGGAGACAAAATTT
2514358 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCAT-TT-CAAGGGAAATGTTTTC-ATGTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT-ATGTTCCAAGGGAAATGTTTTCAATGTT
*
2514420 TATGTTTAAAGAG-AACTGTCTCAAGTGAGACAAAACTTT
65 TATGTTTAAAGAGAAACTGTCTCAAGGGAGACAAAA-TTT
* * *
2514459 CTGTTTCGAGGGAAACTATCTCAAGCGAGATAAAAT
1 -TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
2514495 CTTGTTTTAA
Statistics
Matches: 125, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
100 21 0.17
101 20 0.16
102 48 0.38
103 35 0.28
104 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.30
Consensus pattern (103 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTATGTTCCAAGGGAAATGTTTTCAATGTTT
ATGTTTAAAGAGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:2515417 original size:22 final size:22
Alignment explanation
Indices: 2515392--2515440 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
2515382 TTGTGTTTGG
* *
2515392 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
2515414 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
2515436 TCAAA
1 TCAAA
2515441 AGATTGATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:2515447 original size:22 final size:22
Alignment explanation
Indices: 2515404--2515447 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2515394 AAAGGTTTGG
* * *
2515404 CATTTGATGCTCAAAGGTTTGA
1 CATTGGATGCTCAAAAGATTGA
2515426 CATTGGATGCTCAAAAGATTGA
1 CATTGGATGCTCAAAAGATTGA
2515448 TGGTAGCTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (22 bp):
CATTGGATGCTCAAAAGATTGA
Found at i:2516119 original size:15 final size:16
Alignment explanation
Indices: 2516089--2516166 Score: 61
Period size: 16 Copynumber: 4.9 Consensus size: 16
2516079 TCTTTTTGAT
* *
2516089 TTTTGCTCTTTTTTTC
1 TTTTGTTCTTTGTTTC
2516105 TTTTGTTC-TTGTTTC
1 TTTTGTTCTTTGTTTC
*
2516120 TCTTT-TTCTTTGTTTT
1 T-TTTGTTCTTTGTTTC
* *
2516136 TTTTGCTTTTTTGCTTC
1 TTTTG-TTCTTTGTTTC
* *
2516153 TTTTCTTTTTTGTT
1 TTTTGTTCTTTGTT
2516167 CTTGATTGGA
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
15 13 0.26
16 25 0.50
17 12 0.24
ACGTcount: A:0.00, C:0.14, G:0.09, T:0.77
Consensus pattern (16 bp):
TTTTGTTCTTTGTTTC
Found at i:2519397 original size:18 final size:19
Alignment explanation
Indices: 2519375--2519422 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
2519365 AAATGAGTAA
2519375 AATATAAAAAAGTAAA-AG
1 AATATAAAAAAGTAAATAG
* * * *
2519393 CATATATATAAGTAAATAT
1 AATATAAAAAAGTAAATAG
2519412 AATATAAAAAA
1 AATATAAAAAA
2519423 AAAAGAAAAT
Statistics
Matches: 22, Mismatches: 7, Indels: 1
0.73 0.23 0.03
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (19 bp):
AATATAAAAAAGTAAATAG
Found at i:2519997 original size:34 final size:34
Alignment explanation
Indices: 2519954--2520022 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
2519944 GAATCCTAGC
2519954 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
*
2519988 AAAATTCTATCATATTTTTAGGAGTTTGAATCCT
1 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
2520022 A
1 A
2520023 GTAGGACGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (34 bp):
AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
Found at i:2528795 original size:21 final size:21
Alignment explanation
Indices: 2528749--2528821 Score: 55
Period size: 21 Copynumber: 3.5 Consensus size: 21
2528739 AGTAGGTTTG
2528749 GGATCGATCCCTTTACAAAAAT
1 GGATCGATCCCTTTAC-AAAAT
*
2528771 -GATCGATCCCTTTGAC-CAAT
1 GGATCGATCCCTTT-ACAAAAT
* *
2528791 GGATCAATCTCCTTGA-AAAAT
1 GGATCGATC-CCTTTACAAAAT
*
2528812 -GATTGATCCC
1 GGATCGATCCC
2528822 ATAGATTCCA
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
19 2 0.05
20 9 0.22
21 24 0.59
22 6 0.15
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.29
Consensus pattern (21 bp):
GGATCGATCCCTTTACAAAAT
Found at i:2528850 original size:92 final size:92
Alignment explanation
Indices: 2528658--2528872 Score: 274
Period size: 92 Copynumber: 2.3 Consensus size: 92
2528648 TGGCTCAAAT
*
2528658 GATTGATCCC-TTACAAAAAGAATCGATCCCTTTGACTAATGAATAGATCCCCTTGAAAAAAGGA
1 GATTGATCCCTTTACAAAAAG-ATCGATCCCTTTGACCAATGAATAGATCCCCTTGAAAAAAGGA
* * * * *
2528722 TCGATCTCTTGGATTCTAGTAGGTTTGG
65 TCGATCCCATAGATTCCAATAGGTTTGG
* * * *
2528750 GATCGATCCCTTTACAAAAATGATCGATCCCTTTGACCAATGGATCA-ATCTCCTTG-AAAAATG
1 GATTGATCCCTTTACAAAAA-GATCGATCCCTTTGACCAATGAAT-AGATCCCCTTGAAAAAAGG
*
2528813 ATTGATCCCATAGATTCCAATAGGTTTGG
64 ATCGATCCCATAGATTCCAATAGGTTTGG
*
2528842 GATTGATCCCTTTACAAAAAGATCTATCCCT
1 GATTGATCCCTTTACAAAAAGATCGATCCCT
2528873 CGAGTAAAAT
Statistics
Matches: 107, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
91 10 0.09
92 57 0.53
93 38 0.36
94 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31
Consensus pattern (92 bp):
GATTGATCCCTTTACAAAAAGATCGATCCCTTTGACCAATGAATAGATCCCCTTGAAAAAAGGAT
CGATCCCATAGATTCCAATAGGTTTGG
Found at i:2530720 original size:17 final size:17
Alignment explanation
Indices: 2530667--2530732 Score: 59
Period size: 16 Copynumber: 4.1 Consensus size: 17
2530657 TAAATATAAG
*
2530667 TTCAAAC-ATCCATAAA
1 TTCAAACAATCCACAAA
*
2530683 TTCAAACAAAT--TCAAA
1 TTCAAAC-AATCCACAAA
*
2530699 GTCAAACAATCCACAAA
1 TTCAAACAATCCACAAA
*
2530716 TTCAAACATTCCA-AAA
1 TTCAAACAATCCACAAA
2530732 T
1 T
2530733 ATCCAAAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
15 3 0.08
16 20 0.50
17 15 0.38
18 2 0.05
ACGTcount: A:0.52, C:0.24, G:0.02, T:0.23
Consensus pattern (17 bp):
TTCAAACAATCCACAAA
Found at i:2532632 original size:21 final size:22
Alignment explanation
Indices: 2532608--2532674 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 22
2532598 CAGAACCCCA
2532608 AGGGGGTATCGA-TTCCCCTAC
1 AGGGGGTATCGAGTTCCCCTAC
* *
2532629 AGGGGGAATC-AGTTCCCCTTC
1 AGGGGGTATCGAGTTCCCCTAC
* *
2532650 AAGGGGGGTATCGATTTCCTCTAC
1 -A-GGGGGTATCGAGTTCCCCTAC
2532674 A
1 A
2532675 CTAAAATGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
20 1 0.03
21 17 0.47
22 1 0.03
23 9 0.25
24 8 0.22
ACGTcount: A:0.21, C:0.25, G:0.28, T:0.25
Consensus pattern (22 bp):
AGGGGGTATCGAGTTCCCCTAC
Found at i:2538120 original size:304 final size:304
Alignment explanation
Indices: 2537571--2538182 Score: 1107
Period size: 304 Copynumber: 2.0 Consensus size: 304
2537561 TCATATTCTT
*
2537571 CCAATAGGCATAGTTAGCTTCATTGAAGAAATGAGGCTTGTTGACGAGCATCGAATCGAGACCGG
1 CCAATAGGCATAGTTAGCTCCATTGAAGAAATGAGGCTTGTTGACGAGCATCGAATCGAGACCGG
* *
2537636 AGTCGACGTTTGAAGTGGAGGCCATTGATAACTTTAATTATCGATGTAACTCTTCCCGGATCTAC
66 AGTCGACGTTTGAAGTGGAGGACATTGATAACTTTAATTATCGATGTAACTCTTCCCGGATCTAA
* **
2537701 TCAAGAGATGGTTAAACCTTCAAATGAGTCAAGCTCTGATGCCAATTATTGAGTTAATCGATCTA
131 TCAAGAGACGGTTAAACCTTCAAATGAGTCAAGCTCTGATGAAAATTATTGAGTTAATCGATCTA
*
2537766 TTAATATGGCCAAGAGGGGAGTGAATTGGCAAATAAAAATTCCAGTGGAAGCTTGTGCAGAAAAT
196 TTAATATGGCCAAGAGGGGAGTGAATTGGAAAATAAAAATTCCAGTGGAAGCTTGTGCAGAAAAT
*
2537831 TGAAAGTAATTGCGCAGCGATTTAGAGTGGTTCGACTTTCTCAA
261 TGAAAGTAATTGCGCAGCGATTTAGAGTGGTTCAACTTTCTCAA
*
2537875 CCAATAGGCATAGTTAGCTCCATTGAAGAAATGAGGCTTGTTGACGGGCATCGAATCGAGACCGG
1 CCAATAGGCATAGTTAGCTCCATTGAAGAAATGAGGCTTGTTGACGAGCATCGAATCGAGACCGG
2537940 AGTCGACGTTTGAAGTGGAGGACATTGATAACTTTAATTATCGATGTAACTCTTCCCGGATCTAA
66 AGTCGACGTTTGAAGTGGAGGACATTGATAACTTTAATTATCGATGTAACTCTTCCCGGATCTAA
*
2538005 TCAAGAGACGGTTAAACCTTCAAATGAGTCAAGCTCTGATTAAAATTATTGAGTTAATCGATCTA
131 TCAAGAGACGGTTAAACCTTCAAATGAGTCAAGCTCTGATGAAAATTATTGAGTTAATCGATCTA
* *
2538070 TTAATATGGCCAAGAGGGGGGTGAATTGGAAAATAAAAATTCCGGTGGAAGCTTGTGCAGAAAAT
196 TTAATATGGCCAAGAGGGGAGTGAATTGGAAAATAAAAATTCCAGTGGAAGCTTGTGCAGAAAAT
*
2538135 TGAAAGTAATTGCGCAGCGATTTAGAGTGGTTCAACTTTCTTAA
261 TGAAAGTAATTGCGCAGCGATTTAGAGTGGTTCAACTTTCTCAA
2538179 CCAA
1 CCAA
2538183 AGTCTACGTC
Statistics
Matches: 295, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
304 295 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (304 bp):
CCAATAGGCATAGTTAGCTCCATTGAAGAAATGAGGCTTGTTGACGAGCATCGAATCGAGACCGG
AGTCGACGTTTGAAGTGGAGGACATTGATAACTTTAATTATCGATGTAACTCTTCCCGGATCTAA
TCAAGAGACGGTTAAACCTTCAAATGAGTCAAGCTCTGATGAAAATTATTGAGTTAATCGATCTA
TTAATATGGCCAAGAGGGGAGTGAATTGGAAAATAAAAATTCCAGTGGAAGCTTGTGCAGAAAAT
TGAAAGTAATTGCGCAGCGATTTAGAGTGGTTCAACTTTCTCAA
Found at i:2539041 original size:21 final size:21
Alignment explanation
Indices: 2538999--2539041 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2538989 TTTTCGGGCT
* * *
2538999 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
2539020 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
2539041 A
1 A
2539042 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:2539877 original size:149 final size:146
Alignment explanation
Indices: 2539579--2539879 Score: 557
Period size: 149 Copynumber: 2.0 Consensus size: 146
2539569 GGGTAGAGGG
2539579 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
2539644 ACTTGATCCCTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTATAT
66 ACTTGATCCCTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATAT
2539709 GGCACTACGGTGCAAT
131 GGCACTACGGTGCAAT
2539725 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
2539790 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCC---CTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
2539855 TATGGCACTACGGTGCAAT
128 TATGGCACTACGGTGCAAT
2539874 TCTACG
1 TCTACG
2539880 GGGCACTTTG
Statistics
Matches: 150, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
146 74 0.49
149 76 0.51
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.37
Consensus pattern (146 bp):
TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATAT
GGCACTACGGTGCAAT
Found at i:2540901 original size:20 final size:20
Alignment explanation
Indices: 2540876--2540923 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2540866 TGGAGCGTGG
2540876 GGGGAATCAATACCCCTCAT
1 GGGGAATCAATACCCCTCAT
** *
2540896 GGGGAATCGGTTCCCCTCAT
1 GGGGAATCAATACCCCTCAT
2540916 GGGGAATC
1 GGGGAATC
2540924 GGTTCCCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.27, G:0.29, T:0.21
Consensus pattern (20 bp):
GGGGAATCAATACCCCTCAT
Found at i:2540924 original size:20 final size:20
Alignment explanation
Indices: 2540888--2540930 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
2540878 GGAATCAATA
2540888 CCCCTCATGGGGAATCGGTT
1 CCCCTCATGGGGAATCGGTT
2540908 CCCCTCATGGGGAATCGGTT
1 CCCCTCATGGGGAATCGGTT
2540928 CCC
1 CCC
2540931 TAAGTGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.35, G:0.28, T:0.23
Consensus pattern (20 bp):
CCCCTCATGGGGAATCGGTT
Found at i:2543140 original size:22 final size:23
Alignment explanation
Indices: 2543100--2543142 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2543090 GCAATTTTCT
*
2543100 AAAAAAAGGATCGGCCCCTTTGC
1 AAAAAAAGGATCGACCCCTTTGC
*
2543123 AAAAAAA-GATCGATCCCTTT
1 AAAAAAAGGATCGACCCCTTT
2543143 AGGCCAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (23 bp):
AAAAAAAGGATCGACCCCTTTGC
Found at i:2548124 original size:17 final size:18
Alignment explanation
Indices: 2548091--2548124 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2548081 CCGCTAGTAG
2548091 TGAACCGGTCAGAACCGT
1 TGAACCGGTCAGAACCGT
*
2548109 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
2548125 GACCGACTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.18
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGT
Found at i:2550519 original size:15 final size:16
Alignment explanation
Indices: 2550498--2550533 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2550488 ATCGAATCTG
*
2550498 AAAAAATTAGATATCC
1 AAAAATTTAGATATCC
*
2550514 AAAAATTTGGATATCC
1 AAAAATTTAGATATCC
2550530 AAAA
1 AAAA
2550534 TTTCGAATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.08, T:0.25
Consensus pattern (16 bp):
AAAAATTTAGATATCC
Found at i:2557156 original size:12 final size:12
Alignment explanation
Indices: 2557141--2557169 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
2557131 TGTTTTTCTG
2557141 TTTCTTGTTTTC
1 TTTCTTGTTTTC
2557153 TTTCTTGTTTTC
1 TTTCTTGTTTTC
2557165 TTTCT
1 TTTCT
2557170 AAGCTGGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.76
Consensus pattern (12 bp):
TTTCTTGTTTTC
Found at i:2558035 original size:13 final size:13
Alignment explanation
Indices: 2558019--2558043 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2558009 AGTACGGTAG
2558019 AAAAGAGCTTTTT
1 AAAAGAGCTTTTT
2558032 AAAAGAGCTTTT
1 AAAAGAGCTTTT
2558044 AGAAGTACAA
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:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (13 bp):
AAAAGAGCTTTTT
Found at i:2562472 original size:21 final size:21
Alignment explanation
Indices: 2562433--2562472 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2562423 TTGATTAATA
2562433 AAAAAATATATAGTTATGAAG
1 AAAAAATATATAGTTATGAAG
*
2562454 AAAAATTAT-TAGTTGATGA
1 AAAAAATATATAGTT-ATGA
2562473 TTAGTGTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.33
Consensus pattern (21 bp):
AAAAAATATATAGTTATGAAG
Found at i:2563576 original size:21 final size:22
Alignment explanation
Indices: 2563543--2563593 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 22
2563533 AGAAACTAAT
2563543 TAAAATAATT-AAAAA-CACAAA
1 TAAAAT-ATTAAAAAACCACAAA
2563564 TAATAATATTAAAAAACCACAAA
1 TAA-AATATTAAAAAACCACAAA
2563587 TAAAATA
1 TAAAATA
2563594 AGTAACAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 6 0.22
22 12 0.44
23 9 0.33
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.22
Consensus pattern (22 bp):
TAAAATATTAAAAAACCACAAA
Done.