Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008094.1 Hibiscus syriacus cultivar Beakdansim tig00110610_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: 9952466
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 43
Found at i:1792798 original size:124 final size:122
Alignment explanation
Indices: 1792602--1792837 Score: 339
Period size: 124 Copynumber: 1.9 Consensus size: 122
1792592 AGGTTGAACT
* * * *
1792602 ATGTTGATGTTGATCTATTTCCCTCTGTGATGAGTCGAGCTAAGGTTGAACAAATTCTTCAGATT
1 ATGTTGATGTTGATCTATTTCCCTCTGTGATAAGTCAAGCAAAGGTTGAACAAATTCTTCAGACT
* *
1792667 ATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCAGATTATGAACTCTAGTCTGGAA
66 ATGAACTTATTCTTCCTCTTCAGATAAGTTCTTCAGATTATGAACTCTAGTCTGGAA
* * * *
1792724 ATGTTGATGTTGTTCTATCTT-CTTCTGTGATAAAGTCAAGCAAAAGGTTGAATAATTTCTTCAG
1 ATGTTGATGTTGATCTAT-TTCCCTCTGTGAT-AAGTCAAGC-AAAGGTTGAACAAATTCTTCAG
*
1792788 ACTATGAACTTATTCTTCGTCTTCAGATAAGTTCTTCAGATTATGAACTC
63 ACTATGAACTTATTCTTCCTCTTCAGATAAGTTCTTCAGATTATGAACTC
1792838 CTTTTTCATT
Statistics
Matches: 100, Mismatches: 11, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
122 26 0.26
123 9 0.09
124 65 0.65
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.39
Consensus pattern (122 bp):
ATGTTGATGTTGATCTATTTCCCTCTGTGATAAGTCAAGCAAAGGTTGAACAAATTCTTCAGACT
ATGAACTTATTCTTCCTCTTCAGATAAGTTCTTCAGATTATGAACTCTAGTCTGGAA
Found at i:1792823 original size:39 final size:39
Alignment explanation
Indices: 1792780--1793384 Score: 768
Period size: 39 Copynumber: 15.6 Consensus size: 39
1792770 GTTGAATAAT
** * **
1792780 TTCTTCAGACTATGAACTTATTCTTCGTCTTCAGATAAG
1 TTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAG
* * * * *
1792819 TTCTTCAGATTATGAACTCCTTTTTCATTTTCATACGAG
1 TTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAG
1792858 TTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAG
1 TTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAG
* * *
1792897 TTCTTCAGACTATG-ATTCATTCTTCCTTTTCAGACGAG
1 TTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAG
* * * * * *
1792935 TTCTTCATATTATGAAATACTTCTTCTTCTTCAGATGAG
1 TTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAG
* * *
1792974 TTCTTTAGACTATGAACTCCTTCTTCTTCTTTAGACGAG
1 TTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAG
*
1793013 TTCTTCAGACTATGAACTCCTTCTTTCTCTTCAGACGAG
1 TTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAG
* *
1793052 TTCTTCAGATTATGAACTCATTCTTCCTCTTCAGACGAG
1 TTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAG
* * *
1793091 TTCTTCAAATTATGAACTCATTCTTCCTCTTCAGACGAG
1 TTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAG
* * *
1793130 TTCTTCAGATTATGAACTCCTTCTTTCTCTTCAGACAAG
1 TTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAG
* *
1793169 TTCTTCAGACTATGAACTCCTTCTTCCTCTTCATAAGAG
1 TTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAG
* * * *
1793208 TTCTTCAGATTATGAACTCCTTCTTCCTCTTTATATGAG
1 TTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAG
* *
1793247 TTCTTCAGATTATGAAATCCTTCTTCCTCTTCAGACGAG
1 TTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAG
* * *
1793286 TTCTTCAAACTATGAACTCTTTTTTCCTCTTCAGACGAG
1 TTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAG
* *
1793325 TTCTTCAGACTATGAACT-C--CTTCCTCTTCATATGAG
1 TTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAG
**
1793361 TTCTTCTTACTATGAACTCCTTCT
1 TTCTTCAGACTATGAACTCCTTCT
1793385 GGAAATGTTT
Statistics
Matches: 494, Mismatches: 68, Indels: 8
0.87 0.12 0.01
Matches are distributed among these distances:
36 30 0.06
37 1 0.00
38 33 0.07
39 430 0.87
ACGTcount: A:0.22, C:0.25, G:0.11, T:0.41
Consensus pattern (39 bp):
TTCTTCAGACTATGAACTCCTTCTTCCTCTTCAGACGAG
Found at i:1793096 original size:19 final size:19
Alignment explanation
Indices: 1793072--1793135 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
1793062 TATGAACTCA
1793072 TTCTTCCTCTTCAGACGAG
1 TTCTTCCTCTTCAGACGAG
*** *
1793091 TTCTTCAAATT-ATGAACTCA-
1 TTCTTCCTCTTCA-G-AC-GAG
1793111 TTCTTCCTCTTCAGACGAG
1 TTCTTCCTCTTCAGACGAG
1793130 TTCTTC
1 TTCTTC
1793136 AGATTATGAA
Statistics
Matches: 32, Mismatches: 8, Indels: 10
0.64 0.16 0.20
Matches are distributed among these distances:
18 2 0.06
19 17 0.53
20 11 0.34
21 2 0.06
ACGTcount: A:0.20, C:0.28, G:0.11, T:0.41
Consensus pattern (19 bp):
TTCTTCCTCTTCAGACGAG
Found at i:1794649 original size:54 final size:54
Alignment explanation
Indices: 1794545--1794649 Score: 147
Period size: 54 Copynumber: 1.9 Consensus size: 54
1794535 ATAACTGGTA
* * * * *
1794545 CGTAAAACATTTGACCACACATTCATTATCTCATGTGGTTTCTGCTCAGATGTT
1 CGTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTCTACCCAGATGTT
* *
1794599 CGTAAAACATTTGACAACACATTCATCATTTCTTGTGGCTTCTACCCAGAT
1 CGTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTCTACCCAGAT
1794650 TTCTCAATTA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (54 bp):
CGTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTCTACCCAGATGTT
Found at i:1800128 original size:14 final size:15
Alignment explanation
Indices: 1800108--1800151 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 15
1800098 TGCAAAGATG
1800108 CAAATGTAAAAATGA
1 CAAATGTAAAAATGA
1800123 -AAATGT--AAAT-A
1 CAAATGTAAAAATGA
1800134 CAAATGTAAAAATG-
1 CAAATGTAAAAATGA
1800148 CAAA
1 CAAA
1800152 GATGCGAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
11 1 0.04
12 10 0.40
14 14 0.56
ACGTcount: A:0.61, C:0.07, G:0.11, T:0.20
Consensus pattern (15 bp):
CAAATGTAAAAATGA
Found at i:1802803 original size:12 final size:11
Alignment explanation
Indices: 1802771--1802795 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1802761 GACTAAAATA
1802771 AAATAATAATT
1 AAATAATAATT
1802782 AAATAATAATT
1 AAATAATAATT
1802793 AAA
1 AAA
1802796 GTACTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATAATAATT
Found at i:1805362 original size:19 final size:19
Alignment explanation
Indices: 1805338--1805374 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1805328 ATGACCAACA
*
1805338 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
1805357 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
1805375 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:1806399 original size:24 final size:24
Alignment explanation
Indices: 1806346--1806399 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1806336 GTATTCGAAA
*
1806346 TTTGATCTTGGTTAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* * *
1806370 TATGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1806394 TTTGAT
1 TTTGAT
1806400 GATGTTTCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1808683 original size:18 final size:18
Alignment explanation
Indices: 1808660--1808694 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1808650 AGAAAAAGGC
*
1808660 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
1808678 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
1808695 CAACTGGCTT
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:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:1808890 original size:20 final size:20
Alignment explanation
Indices: 1808865--1809064 Score: 181
Period size: 20 Copynumber: 10.6 Consensus size: 20
1808855 TTACACATTC
*
1808865 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1808885 ATTTGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
* * * *
1808904 A----A-AATTGCAATGCAA
1 ATTTGACTATCGCAACGCGA
*
1808919 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
1808939 ATTTGACTATCGCAACAC-A
1 ATTTGACTATCGCAACGCGA
* *
1808958 A----A-AATTGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1808973 ATTTGACTATTGCAACGCGA
1 ATTTGACTATCGCAACGCGA
1808993 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
1809013 ATATGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* * *
1809033 ATTTCATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
1809053 ATTTGACTATCG
1 ATTTGACTATCG
1809065 TAACTAGAAA
Statistics
Matches: 146, Mismatches: 22, Indels: 24
0.76 0.11 0.12
Matches are distributed among these distances:
14 16 0.11
15 6 0.04
19 6 0.04
20 118 0.81
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:1808947 original size:54 final size:54
Alignment explanation
Indices: 1808865--1809064 Score: 238
Period size: 54 Copynumber: 3.6 Consensus size: 54
1808855 TTACACATTC
* *
1808865 ATTTGAATATCGCAACGCGAATTTGACTATCGCAACGCAAAAATTGCAATGCAA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAAATTGCAACGCAA
* * *
1808919 ATTTGACTATCGCAACACGAATTTGACTATCGCAACACAAAAATTGCAACGCGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAAATTGCAACGCAA
* * **
1808973 ATTTGACTATTGCAACGCGAATTTGACTATCGCAACGCGAATATGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGC-AA-A--A--ATTGCAACGCAA
* * *
1809033 ATTTCATTATCGCAACGGGAATTTGACTATCG
1 ATTTGACTATCGCAACGCGAATTTGACTATCG
1809065 TAACTAGAAA
Statistics
Matches: 126, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
54 84 0.67
55 2 0.02
56 1 0.01
58 1 0.01
60 38 0.30
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.26
Consensus pattern (54 bp):
ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCAAAAATTGCAACGCAA
Found at i:1809137 original size:20 final size:20
Alignment explanation
Indices: 1809108--1809171 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
1809098 GCAATGCGAA
*
1809108 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCATTGCGATT
*
1809128 TTGGCTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
*
1809148 TTGACTTTCGCATTGTGATT
1 TTGACTTTCGCATTGCGATT
1809168 TTGA
1 TTGA
1809172 GTTTAGCGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.12, C:0.17, G:0.23, T:0.47
Consensus pattern (20 bp):
TTGACTTTCGCATTGCGATT
Found at i:1809326 original size:14 final size:14
Alignment explanation
Indices: 1809307--1809341 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1809297 TCAATTAAAG
*
1809307 AAATCAACTTTTAC
1 AAATCAAATTTTAC
1809321 AAATCAAATTTTAC
1 AAATCAAATTTTAC
1809335 AAATCAA
1 AAATCAA
1809342 TTAAACAAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATCAAATTTTAC
Found at i:1810740 original size:21 final size:21
Alignment explanation
Indices: 1810716--1810838 Score: 83
Period size: 21 Copynumber: 5.9 Consensus size: 21
1810706 GTGAATTAGG
* * *
1810716 CTCTTGAATGGTGAGAGGGAC
1 CTCTTGAACGATGACAGGGAC
* *
1810737 CTCTTCAACGATGACAGGGGC
1 CTCTTGAACGATGACAGGGAC
1810758 CTCTTGAACGATAGGA-AGGGA-
1 CTCTTGAACGAT--GACAGGGAC
* ** * *
1810779 GTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGATGACAGGGAC
*
1810800 CTCTTGAACGAT-AGGAGAGG-C
1 CTCTTGAACGATGA-CAG-GGAC
1810821 CTCTTGAACGATGACAGG
1 CTCTTGAACGATGACAGG
1810839 TGAGTCGGGC
Statistics
Matches: 79, Mismatches: 16, Indels: 15
0.72 0.15 0.14
Matches are distributed among these distances:
19 2 0.03
20 6 0.08
21 62 0.78
22 7 0.09
23 2 0.03
ACGTcount: A:0.26, C:0.18, G:0.35, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATGACAGGGAC
Found at i:1810826 original size:42 final size:42
Alignment explanation
Indices: 1810746--1810838 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 42
1810736 CCTCTTCAAC
*
1810746 GATGACAGGGGCCTCTTGAACGATAGGAAGGGAGTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATAGGAAGGGACTCTTGAGG
* * **
1810788 GATGATAGGGGCCTCTTGAACGATAGG-AGAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGATAGGAAG-GGACTCTTGAGG
1810830 GATGACAGG
1 GATGACAGG
1810839 TGAGTCGGGC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
41 2 0.05
42 42 0.95
ACGTcount: A:0.27, C:0.16, G:0.38, T:0.19
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATAGGAAGGGACTCTTGAGG
Found at i:1811191 original size:20 final size:20
Alignment explanation
Indices: 1811166--1811210 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1811156 CATATAGTTC
*
1811166 TGAAACTTAAAATCGTAACA
1 TGAAACTTAAAATCGCAACA
1811186 TGAAACTTAAAATCGCAACA
1 TGAAACTTAAAATCGCAACA
*
1811206 CGAAA
1 TGAAA
1811211 ATGACTACCG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.51, C:0.18, G:0.11, T:0.20
Consensus pattern (20 bp):
TGAAACTTAAAATCGCAACA
Found at i:1811245 original size:20 final size:20
Alignment explanation
Indices: 1811197--1811265 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
1811187 GAAACTTAAA
* *
1811197 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGGAAATGACT
*
1811217 ACCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* *
1811237 ATCGCAACG-TGAATTTGACT
1 ATCGCAACGCGGAA-ATGACT
1811257 ATCGCAACG
1 ATCGCAACG
1811266 GGATAATCGC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 3 0.07
20 39 0.93
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:1811296 original size:33 final size:34
Alignment explanation
Indices: 1811257--1811332 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 34
1811247 GAATTTGACT
*
1811257 ATCGCAACGGGATAATCGCAATGCG-AAATAAAA
1 ATCGCAACGGGAAAATCGCAATGCGAAAATAAAA
* *
1811290 ATCGCAACGTGAAAATCGCAATGCGAAAATGAAA
1 ATCGCAACGGGAAAATCGCAATGCGAAAATAAAA
1811324 ATCGCAACG
1 ATCGCAACG
1811333 CGAATTTAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 23 0.59
34 16 0.41
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.14
Consensus pattern (34 bp):
ATCGCAACGGGAAAATCGCAATGCGAAAATAAAA
Found at i:1811322 original size:20 final size:20
Alignment explanation
Indices: 1811299--1811336 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1811289 AATCGCAACG
*
1811299 TGAAAATCGCAATGCGAAAA
1 TGAAAATCGCAACGCGAAAA
1811319 TGAAAATCGCAACGCGAA
1 TGAAAATCGCAACGCGAA
1811337 TTTAGTTTCG
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:0.47, C:0.18, G:0.21, T:0.13
Consensus pattern (20 bp):
TGAAAATCGCAACGCGAAAA
Found at i:1811354 original size:19 final size:20
Alignment explanation
Indices: 1811332--1811457 Score: 91
Period size: 20 Copynumber: 6.4 Consensus size: 20
1811322 AAATCGCAAC
1811332 GCGA-ATTTAGTTTCGCGTT
1 GCGATATTTAGTTTCGCGTT
* *
1811351 GCGAT-TTTGGTTTCTCGTT
1 GCGATATTTAGTTTCGCGTT
* *
1811370 GCGATTTTTA-TTTCGCATT
1 GCGATATTTAGTTTCGCGTT
* *
1811389 GCGATAGTCA-TTTCCGCGTT
1 GCGATATTTAGTTT-CGCGTT
* * * *
1811409 GCGATAGTCATTTTCGTGTT
1 GCGATATTTAGTTTCGCGTT
*
1811429 GCGAT-TTTAAGTTTCGTGTT
1 GCGATATTT-AGTTTCGCGTT
1811449 GCGACTATT
1 GCGA-TATT
1811458 CTTCTTCTAC
Statistics
Matches: 87, Mismatches: 13, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
19 39 0.45
20 42 0.48
21 4 0.05
22 2 0.02
ACGTcount: A:0.14, C:0.17, G:0.24, T:0.45
Consensus pattern (20 bp):
GCGATATTTAGTTTCGCGTT
Found at i:1813361 original size:20 final size:20
Alignment explanation
Indices: 1813338--1813393 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
1813328 TCTGAAACTT
1813338 AAAATCGCAACATGAAAATG
1 AAAATCGCAACATGAAAATG
* *
1813358 AAAATCGAAACACGAAAATG
1 AAAATCGCAACATGAAAATG
** *
1813378 ACTATCGCAACGTGAA
1 AAAATCGCAACATGAA
1813394 TTTGACTATC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.52, C:0.18, G:0.16, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACATGAAAATG
Found at i:1813904 original size:22 final size:22
Alignment explanation
Indices: 1813851--1813897 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1813841 GAGATAGATG
*
1813851 GATTTCGCCGGAGATGGGGACA
1 GATTTCGTCGGAGATGGGGACA
1813873 GATTTCGTCGGAGATGGGGACA
1 GATTTCGTCGGAGATGGGGACA
1813895 GAT
1 GAT
1813898 GTTGTCGTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.23, C:0.15, G:0.40, T:0.21
Consensus pattern (22 bp):
GATTTCGTCGGAGATGGGGACA
Found at i:1814097 original size:20 final size:20
Alignment explanation
Indices: 1814072--1814257 Score: 144
Period size: 20 Copynumber: 9.2 Consensus size: 20
1814062 TTATAGCAAC
1814072 GCGATTGTCAGAATCGCGTT
1 GCGATTGTCAGAATCGCGTT
*
1814092 GCGATTGTCAGAATCACGTT
1 GCGATTGTCAGAATCGCGTT
* ** *
1814112 GTGATTATGT-ATTATAGCGTT
1 GCGA-T-TGTCAGAATCGCGTT
*
1814133 GCGATAGTCAGAATCGCGTT
1 GCGATTGTCAGAATCGCGTT
*
1814153 GCGATAGTCAGAATCGCGTT
1 GCGATTGTCAGAATCGCGTT
* *
1814173 GCGATT-TACATATTCGCGTT
1 GCGATTGT-CAGAATCGCGTT
* * *
1814193 GCGATT-TACATATTCGCATT
1 GCGATTGT-CAGAATCGCGTT
* * **
1814213 GCGATTTTCTAAAATCGCAAT
1 GCGATTGTC-AGAATCGCGTT
* *
1814234 GCGATAGTCAAAATCGCGTT
1 GCGATTGTCAGAATCGCGTT
1814254 GCGA
1 GCGA
1814258 ATCTGGAAAC
Statistics
Matches: 138, Mismatches: 22, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
19 3 0.02
20 105 0.76
21 27 0.20
22 3 0.02
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.32
Consensus pattern (20 bp):
GCGATTGTCAGAATCGCGTT
Found at i:1814153 original size:61 final size:61
Alignment explanation
Indices: 1814049--1814178 Score: 188
Period size: 61 Copynumber: 2.1 Consensus size: 61
1814039 GAAAATCGCA
* * *
1814049 TTGCGATTTTGTATTATAGCAACGCGATTGTCAGAATCGCGTTGCGATTGTCAGAATCACG
1 TTGCGATTATGTATTATAGCAACGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCACG
* *** *
1814110 TTGTGATTATGTATTATAGCGTTGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCGCG
1 TTGCGATTATGTATTATAGCAACGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCACG
1814171 TTGCGATT
1 TTGCGATT
1814179 TACATATTCG
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (61 bp):
TTGCGATTATGTATTATAGCAACGCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCACG
Found at i:1814897 original size:22 final size:23
Alignment explanation
Indices: 1814863--1814905 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1814853 ATATAATAAA
1814863 TAATATTATTTATTATAAAAACT
1 TAATATTATTTATTATAAAAACT
*
1814886 TAATATTA-TTATTTTAAAAA
1 TAATATTATTTATTATAAAAA
1814906 TATTATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TAATATTATTTATTATAAAAACT
Found at i:1815073 original size:21 final size:21
Alignment explanation
Indices: 1815048--1815133 Score: 59
Period size: 21 Copynumber: 4.0 Consensus size: 21
1815038 TCTATAAAAA
1815048 TAAAAATATTATATTATATTT
1 TAAAAATATTATATTATATTT
* *
1815069 TAAAATTATTAATAAATATATTT
1 TAAAAATATT-AT-ATTATATTT
* * *
1815092 TAAGGAAT-TTTTATAATATTAT
1 TAA-AAATATTATATTATATT-T
*
1815114 T-AGAATATTATATTAATATT
1 TAAAAATATTATATT-ATATT
1815134 AAATACATAA
Statistics
Matches: 50, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
20 4 0.08
21 21 0.42
22 10 0.20
23 13 0.26
24 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (21 bp):
TAAAAATATTATATTATATTT
Found at i:1815109 original size:23 final size:22
Alignment explanation
Indices: 1815048--1815110 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
1815038 TCTATAAAAA
* *
1815048 TAAAAATA-TTATATTATATTT
1 TAAAATTATTTATAATATATTT
*
1815069 TAAAATTATTAATAAATATATTT
1 TAAAATTATTTAT-AATATATTT
1815092 TAAGGAATT-TTTATAATAT
1 TAA--AATTATTTATAATAT
1815111 TATTAGAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 7 0.21
22 3 0.09
23 16 0.47
24 4 0.12
25 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (22 bp):
TAAAATTATTTATAATATATTT
Found at i:1815274 original size:13 final size:13
Alignment explanation
Indices: 1815244--1815351 Score: 58
Period size: 13 Copynumber: 9.0 Consensus size: 13
1815234 TTAAAATAAG
* *
1815244 AATATAATAGTAT
1 AATATATTATTAT
*
1815257 CATATATTATTAT
1 AATATATTATTAT
*
1815270 AATATA--ATT-G
1 AATATATTATTAT
*
1815280 AATATATTATTGT
1 AATATATTATTAT
1815293 AATA-ATATATT-T
1 AATATAT-TATTAT
1815305 -ATA-A-T-TTAT
1 AATATATTATTAT
*
1815314 ATTATATTATTAAT
1 AATATATTATT-AT
*
1815328 AA-ATATTAATA-
1 AATATATTATTAT
1815339 AATATATTATTAT
1 AATATATTATTAT
1815352 TATCATATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 24
0.68 0.09 0.22
Matches are distributed among these distances:
8 2 0.03
9 2 0.03
10 8 0.11
11 10 0.14
12 16 0.22
13 32 0.44
14 3 0.04
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (13 bp):
AATATATTATTAT
Found at i:1815370 original size:45 final size:41
Alignment explanation
Indices: 1815292--1815379 Score: 115
Period size: 42 Copynumber: 2.0 Consensus size: 41
1815282 TATATTATTG
1815292 TAATAATATATTTATAATTTATATTATATTATTAATAAATAT
1 TAATAATATATTTATAATTTATATTATATTATTAA-AAATAT
*
1815334 TAATAA-ATATATTATTATTATCATATTTATATTATTAAAAATAT
1 TAATAATATAT-TTATAATT-T-ATA-TTATATTATTAAAAATAT
1815378 TA
1 TA
1815380 TTATTAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
41 4 0.10
42 13 0.32
43 1 0.02
44 11 0.27
45 12 0.29
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (41 bp):
TAATAATATATTTATAATTTATATTATATTATTAAAAATAT
Found at i:1815402 original size:2 final size:2
Alignment explanation
Indices: 1815395--1815420 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1815385 AAAATTTTTA
1815395 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1815421 TTATCACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1816563 original size:25 final size:25
Alignment explanation
Indices: 1816529--1816578 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1816519 TGTTAACTAT
**
1816529 TGTTAACTATTAATTGTTAATCGTC
1 TGTTAACTATTAATCATTAATCGTC
1816554 TGTTAACTATTAATCATTAATCGTC
1 TGTTAACTATTAATCATTAATCGTC
1816579 AATGACCGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (25 bp):
TGTTAACTATTAATCATTAATCGTC
Found at i:1816993 original size:29 final size:29
Alignment explanation
Indices: 1816961--1817094 Score: 105
Period size: 29 Copynumber: 4.7 Consensus size: 29
1816951 GTATATATCA
* *
1816961 TTATTGTAATTTATAAGAAGTTTTGATTT
1 TTATTGTAATTTATAAAAAGGTTTGATTT
* * *
1816990 TTATTATGATTTATAAAAAGGTTTG-TCCT
1 TTATTGTAATTTATAAAAAGGTTTGAT-TT
* * *
1817019 TTATTTTAATTTACAATAAGGTTT-A-TT
1 TTATTGTAATTTATAAAAAGGTTTGATTT
* * *
1817046 TTATTGTAATTTACAAAATGGTTTG-TCAT
1 TTATTGTAATTTATAAAAAGGTTTGAT-TT
* *
1817075 TTATTATAATTTACAAAAAG
1 TTATTGTAATTTATAAAAAG
1817095 ATTTATCCTT
Statistics
Matches: 84, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
27 22 0.26
28 1 0.01
29 61 0.73
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.50
Consensus pattern (29 bp):
TTATTGTAATTTATAAAAAGGTTTGATTT
Found at i:1817069 original size:56 final size:56
Alignment explanation
Indices: 1816961--1817100 Score: 154
Period size: 56 Copynumber: 2.5 Consensus size: 56
1816951 GTATATATCA
* * * * * * *
1816961 TTATTGTAATTTATAAGAAGTTTTGATTTTTATTATGATTTATAAAAAGGTTTGTCCT
1 TTATTATAATTTACAAAAAGATTT-A-TTTTATTATAATTTACAAAAAGGTTTGTCAT
* * * * *
1817019 TTATTTTAATTTACAATAAGGTTTATTTTATTGTAATTTACAAAATGGTTTGTCAT
1 TTATTATAATTTACAAAAAGATTTATTTTATTATAATTTACAAAAAGGTTTGTCAT
1817075 TTATTATAATTTACAAAAAGATTTAT
1 TTATTATAATTTACAAAAAGATTTAT
1817101 CCTTTAATTT
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
56 49 0.70
57 1 0.01
58 20 0.29
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.51
Consensus pattern (56 bp):
TTATTATAATTTACAAAAAGATTTATTTTATTATAATTTACAAAAAGGTTTGTCAT
Found at i:1817106 original size:29 final size:29
Alignment explanation
Indices: 1816989--1817115 Score: 134
Period size: 29 Copynumber: 4.4 Consensus size: 29
1816979 AGTTTTGATT
* * *
1816989 TTTATTATGATTTATAAAAAGGTTTGTCC
1 TTTATTATAATTTACAAAAAGGTTTATCC
* *
1817018 TTTATTTTAATTTACAATAAGGTTTAT--
1 TTTATTATAATTTACAAAAAGGTTTATCC
* * * *
1817045 TTTATTGTAATTTACAAAATGGTTTGTCA
1 TTTATTATAATTTACAAAAAGGTTTATCC
*
1817074 TTTATTATAATTTACAAAAAGATTTATCC
1 TTTATTATAATTTACAAAAAGGTTTATCC
1817103 TTTAATT-TAATTT
1 TTT-ATTATAATTT
1817116 TTAAAAATAG
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
27 23 0.28
29 55 0.68
30 3 0.04
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51
Consensus pattern (29 bp):
TTTATTATAATTTACAAAAAGGTTTATCC
Found at i:1818810 original size:3 final size:3
Alignment explanation
Indices: 1818802--1818905 Score: 199
Period size: 3 Copynumber: 34.7 Consensus size: 3
1818792 CTACAAAGTT
1818802 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
1818850 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1818898 ATA ATA AT
1 ATA ATA AT
1818906 GTCTAAAAGT
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 99 1.00
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1819937 original size:29 final size:29
Alignment explanation
Indices: 1819864--1819962 Score: 128
Period size: 29 Copynumber: 3.3 Consensus size: 29
1819854 ATTTAAGCAT
*
1819864 CTAAAGTATTTTTTTGGTCAAAA-AAGTAC
1 CTAAAGTATTTTTTT-GTCAAAATAGGTAC
*
1819893 CTAGAGTTATCTTTTTTGTCAAAATAGGTAC
1 CTAAAG-TAT-TTTTTTGTCAAAATAGGTAC
**
1819924 CTAAAGTATTTTTTAATCAAAATAGGTAC
1 CTAAAGTATTTTTTTGTCAAAATAGGTAC
1819953 CTAAAGTATT
1 CTAAAGTATT
1819963 CATTTTTTCA
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
29 33 0.53
30 13 0.21
31 16 0.26
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.39
Consensus pattern (29 bp):
CTAAAGTATTTTTTTGTCAAAATAGGTAC
Found at i:1819990 original size:58 final size:57
Alignment explanation
Indices: 1819823--1819998 Score: 158
Period size: 60 Copynumber: 3.0 Consensus size: 57
1819813 CTTATATAAC
* * * **
1819823 AAATAAGTACCTAAAGTATGTTCTCTTTTTCATTTAAGCATCTAAAGTATTTTTTTGGTCA
1 AAATAAGTACCTAAAGTA--TTCT-TTTTTCATATAAGTACCTAAAGTA-TTTTTTAATCA
* * *
1819884 AAA-AAGTACCTAGAGT-TATCTTTTTTGTCAAAATAGGTACCTAAAGTATTTTTTAATCA
1 AAATAAGTACCTAAAGTAT-TC-TTTTT-TC-ATATAAGTACCTAAAGTATTTTTTAATCA
* * *
1819943 AAATAGGTACCTAAAGTATTCATTTTTTCATCTAAGTACCTAAAGTATTCTTTAAT
1 AAATAAGTACCTAAAGTATTC-TTTTTTCATATAAGTACCTAAAGTATTTTTTAAT
1819999 TAACACTTAT
Statistics
Matches: 94, Mismatches: 15, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
57 1 0.01
58 29 0.31
59 17 0.18
60 43 0.46
61 4 0.04
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (57 bp):
AAATAAGTACCTAAAGTATTCTTTTTTCATATAAGTACCTAAAGTATTTTTTAATCA
Found at i:1820046 original size:29 final size:29
Alignment explanation
Indices: 1820014--1820093 Score: 81
Period size: 31 Copynumber: 2.7 Consensus size: 29
1820004 CTTATATAAC
*
1820014 AAATAAGTACTTAAAGTATTTTTTTATCA
1 AAATAAGTACTTAAAGTATTTTTTGATCA
* *
1820043 AAATAAGTA-TGTAAACTTATCTTTTTGGTCA
1 AAATAAGTACT-TAAA-GTAT-TTTTTGATCA
* *
1820074 AAATAGGTACCTAAAGTATT
1 AAATAAGTACTTAAAGTATT
1820094 CAATTTTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
28 1 0.02
29 14 0.34
30 6 0.15
31 20 0.49
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (29 bp):
AAATAAGTACTTAAAGTATTTTTTGATCA
Found at i:1820207 original size:28 final size:28
Alignment explanation
Indices: 1820175--1820278 Score: 127
Period size: 28 Copynumber: 3.6 Consensus size: 28
1820165 AAAAAAATTG
* *
1820175 AATACTTTAGGTACCTATTTTGACCGAA
1 AATACTTTAGGTACTTATTTTGACCAAA
*
1820203 AATACTTTAAGTACTTATTTTGACTCAAA
1 AATACTTTAGGTACTTATTTTGAC-CAAA
* *
1820232 AGATAAGTTTAGGTACTTCTTTTGACCAAA
1 A-AT-ACTTTAGGTACTTATTTTGACCAAA
*
1820262 AATACTTTAGGAACTTA
1 AATACTTTAGGTACTTA
1820279 GATGAAAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
28 33 0.52
29 6 0.09
30 7 0.11
31 18 0.28
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (28 bp):
AATACTTTAGGTACTTATTTTGACCAAA
Found at i:1820410 original size:28 final size:28
Alignment explanation
Indices: 1820374--1820477 Score: 113
Period size: 30 Copynumber: 3.6 Consensus size: 28
1820364 AAAATGTTTG
* * * *
1820374 AATAGTTTAGGTACCTAGTTTGACATAA
1 AATACTTTAGGTACTTATTTTGACAAAA
1820402 AATACTTTA-GT-CGTTTATTTTGACAAAAA
1 AATACTTTAGGTAC--TTATTTTGAC-AAAA
1820431 AATAACTTTAGGTACTTATTTTGATCAAAA
1 AAT-ACTTTAGGTACTTATTTTGA-CAAAA
1820461 AATACTTTAGGTACTTA
1 AATACTTTAGGTACTTA
1820478 AATGAAAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
26 1 0.02
27 2 0.03
28 16 0.25
29 20 0.31
30 22 0.34
31 3 0.05
32 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (28 bp):
AATACTTTAGGTACTTATTTTGACAAAA
Found at i:1820460 original size:29 final size:28
Alignment explanation
Indices: 1820379--1820477 Score: 89
Period size: 29 Copynumber: 3.4 Consensus size: 28
1820369 GTTTGAATAG
* *
1820379 TTTAGGTACCTAGTTTGACATAAAAT-AC
1 TTTAGGTACTTATTTTGACA-AAAATAAC
1820407 TTTA-GT-CGTTTATTTTGACAAAAAAATAAC
1 TTTAGGTAC--TTATTTTGAC--AAAAATAAC
1820437 TTTAGGTACTTATTTTGATCAAAAA-ATAC
1 TTTAGGTACTTATTTTGA-CAAAAATA-AC
1820466 TTTAGGTACTTA
1 TTTAGGTACTTA
1820478 AATGAAAAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 17
0.76 0.03 0.22
Matches are distributed among these distances:
26 1 0.02
27 2 0.03
28 13 0.22
29 24 0.40
30 16 0.27
31 3 0.05
32 1 0.02
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.40
Consensus pattern (28 bp):
TTTAGGTACTTATTTTGACAAAAATAAC
Found at i:1826429 original size:21 final size:21
Alignment explanation
Indices: 1826405--1826463 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
1826395 TGATTTATTA
1826405 TTATGGATTTCAAGTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
*
1826426 TTATGGATTTCAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
*
1826447 TTATGGATATCAAGTTT
1 TTATGGATTTCAAGTTT
1826464 ATTGGATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.22, C:0.07, G:0.20, T:0.51
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:1826859 original size:42 final size:42
Alignment explanation
Indices: 1826803--1826887 Score: 109
Period size: 41 Copynumber: 2.0 Consensus size: 42
1826793 TAGTGATGTT
* * *
1826803 TAAAAAAACTGCCGCTAAATATCTTAACATTTAGTGGCGTTTG
1 TAAAAAAACTGCCGCTAAA-AACATAACATTTAGCGGCGTTTG
* *
1826846 TAAAAATAC-GCCGCTAAAAACATAACCTTTAGCGGCGTTTG
1 TAAAAAAACTGCCGCTAAAAACATAACATTTAGCGGCGTTTG
1826887 T
1 T
1826888 TTCAGCAGCG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
41 20 0.54
42 9 0.24
43 8 0.22
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29
Consensus pattern (42 bp):
TAAAAAAACTGCCGCTAAAAACATAACATTTAGCGGCGTTTG
Found at i:1829293 original size:17 final size:16
Alignment explanation
Indices: 1829272--1829303 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1829262 AAAATTAATT
1829272 TTTTTTCTTATAAAAC
1 TTTTTTCTTATAAAAC
*
1829288 TTTTTTCTTATCAAAC
1 TTTTTTCTTATAAAAC
1829304 AAGTGATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.16, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTTTCTTATAAAAC
Found at i:1834425 original size:35 final size:34
Alignment explanation
Indices: 1834341--1834425 Score: 93
Period size: 35 Copynumber: 2.4 Consensus size: 34
1834331 AATATAATTT
*
1834341 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
1834375 TAAATAATAAAAAAATTACAATAACTTGTATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA---GTATTAAATGG
1834413 T-AATA-AACAAAAT
1 TAAATACAACAAAAT
1834426 CAACAAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
34 5 0.12
35 22 0.51
36 1 0.02
37 3 0.07
38 12 0.28
ACGTcount: A:0.56, C:0.08, G:0.07, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:1836743 original size:12 final size:12
Alignment explanation
Indices: 1836726--1836782 Score: 59
Period size: 11 Copynumber: 5.1 Consensus size: 12
1836716 AAAAAAATTA
1836726 ATTAAATAAAAT
1 ATTAAATAAAAT
*
1836738 ATT-AA-AATA-
1 ATTAAATAAAAT
1836747 ATTAAATAAAAT
1 ATTAAATAAAAT
*
1836759 ACT-AATAAAAT
1 ATTAAATAAAAT
*
1836770 ATTAAATATAAT
1 ATTAAATAAAAT
1836782 A
1 A
1836783 AAATATACCC
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
9 3 0.08
10 5 0.14
11 15 0.42
12 13 0.36
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (12 bp):
ATTAAATAAAAT
Found at i:1836750 original size:21 final size:23
Alignment explanation
Indices: 1836719--1836782 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 23
1836709 AACTGCAAAA
1836719 AAAATTAATTAAATAAAATA-T-T
1 AAAA-TAATTAAATAAAATACTAT
1836741 AAAATAATTAAATAAAATACTAAT
1 AAAATAATTAAATAAAATACT-AT
*
1836765 AAAAT-ATTAAATATAATA
1 AAAATAATTAAATAAAATA
1836783 AAATATACCC
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
21 15 0.39
22 5 0.13
23 12 0.32
24 6 0.16
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAATAATTAAATAAAATACTAT
Found at i:1839150 original size:23 final size:23
Alignment explanation
Indices: 1839124--1839175 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
1839114 AATAACATAT
**
1839124 TAGGTAGCGCTTATATAATATGA
1 TAGGTAGCGCTTATATAATAAAA
*
1839147 TAGGTAGCGTTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
1839170 TAGGTA
1 TAGGTA
1839176 TTTAACCGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:1839248 original size:87 final size:87
Alignment explanation
Indices: 1839088--1839249 Score: 243
Period size: 87 Copynumber: 1.9 Consensus size: 87
1839078 ATATTATATC
* * *
1839088 ATTTAATCAGAAATATTATTAAGTACAATAACATATTAGGTAGCGCTTATATAATATGATAGGTA
1 ATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATATAATAGGTA
**
1839153 GCGTTTATATAATAAAATAGGT
66 GCACTTATATAATAAAATAGGT
* * * *
1839175 ATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGTGTTTATATAATGTAATAGGTA
1 ATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATATAATAGGTA
1839240 GCACTTATAT
66 GCACTTATAT
1839250 TGACCTATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 66 1.00
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (87 bp):
ATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATATAATAGGTA
GCACTTATATAATAAAATAGGT
Found at i:1839616 original size:199 final size:199
Alignment explanation
Indices: 1839267--1839773 Score: 598
Period size: 199 Copynumber: 2.5 Consensus size: 199
1839257 TTTTCTAAGT
* * *
1839267 AAACCGGTATATTTATACCT-GTAACATTGCAAATTTACCTATTACATTATAATTATCGGTTTCG
1 AAACCGATATATTTATATCTGGT-ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCG
* ** * *
1839331 ATGTTTTTTTGGATCAATAGAATTT--TAAATGTATCAACACTTTATGCATGCACCTCGTTGGGC
65 ATG-TTTTGTGGATCAATA-CTTTTAATAAATGTATCGACACTTTATGCATGCACCCCGTTGGGC
* * * * * *
1839394 ATTCATTCTGGAAAAAGGTATCGATACAAACTTAAAAAG-TGTCGATACATTAT-TTAGACTTAT
128 ATTAATTATGGAAAAAAGTATCGACACAAA-TTAAAAAGATGTCGATACATTATGCTA-ACATAT
1839457 TTTCTCATA
191 TTTCTCATA
* * * *
1839466 AAACCGATATATTTCTATCTGGTACATTGTAAATTTACCTATCACATTGTAA-TATTGGTTTCGA
1 AAACCGATATATTTATATCTGGTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
* * * * * *
1839530 TGTTTGGTGGATCGATACTTTTAATAAATGTATGGACACTTTATGCGTGTACCCCGTTTGGCATT
66 TGTTTTGTGGATCAATACTTTTAATAAATGTATCGACACTTTATGCATGCACCCCGTTGGGCATT
* * *
1839595 AATTATGGACAAAAAGTATCGACACAAATTTAAATGATGTCGATACTTTATGCTAACATATTTTC
131 AATTATGGA-AAAAAGTATCGACACAAATTAAAAAGATGTCGATACATTATGCTAACATATTTTC
*
1839660 TTATA
195 TCATA
* *
1839665 AAACC-AGTATATTTATATCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCG
1 AAACCGA-TATATTTATATCTGGTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCG
* *
1839729 ATGTTATTG-GGATTAATACTTTTAATAAATGTATCGACAGTTTAT
65 ATGTT-TTGTGGATCAATACTTTTAATAAATGTATCGACACTTTAT
1839774 ATTCTGGACA
Statistics
Matches: 260, Mismatches: 39, Indels: 17
0.82 0.12 0.05
Matches are distributed among these distances:
196 3 0.01
197 12 0.05
198 62 0.24
199 130 0.50
200 51 0.20
201 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (199 bp):
AAACCGATATATTTATATCTGGTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
TGTTTTGTGGATCAATACTTTTAATAAATGTATCGACACTTTATGCATGCACCCCGTTGGGCATT
AATTATGGAAAAAAGTATCGACACAAATTAAAAAGATGTCGATACATTATGCTAACATATTTTCT
CATA
Found at i:1842470 original size:19 final size:19
Alignment explanation
Indices: 1842425--1842473 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
1842415 TTACATTCAC
1842425 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
** *
1842444 ATGTAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1842463 ATACAAAATTA
1 ATACAAAATTA
1842474 ACCCTACATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1844586 original size:199 final size:198
Alignment explanation
Indices: 1843894--1844855 Score: 1032
Period size: 199 Copynumber: 4.9 Consensus size: 198
1843884 CACGTTATTT
* * * *
1843894 AAAAAGTATCGACACAAATTTAAAAGTGTCGATACATTATATTA-ACATATTCTCTCATAAAACC
1 AAAAAGTATCGACACAAATTCAAAAGTGTCGATACATTAT-GTAGACCTATTCTCACATAAAACC
* * *
1843958 GGTATATTTATACCAGTTACATTGTAAATTTACATATTACGTTATAATTATCGGTTTCGATGTTT
65 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
** * * * * *
1844023 TTGGGATCGATACAATTTAT-AATGTATCGACACTTTCTGCCTGCACCCCGTTTGACATTCATTC
130 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCA-CCAGTTTGGCATTCATTT
1844087 TGGAC
194 TGGAC
* ** *
1844092 AAAATGTATCGACACAAA-TCTAAAACGTGTCGATACATTATGTTCACCTATTTTCTA-ATAAAA
1 AAAAAGTATCGACACAAATTC-AAAA-GTGTCGATACATTATGTAGACCTATTCTC-ACATAAAA
** * * * * *
1844155 CAAGTAAATTTATACCGGTTAAATTGTAAATTTACGTATTACATTATAATAATCGGTTTTGATGT
63 CCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGT
* * * * ** *
1844220 TTTTGGAATTGATACTTTTTAAAAATGTATCGATACTTTATGCGTGCAACCCTTTTGGTATTCAT
128 TTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGC-ACCAGTTTGGCATTCAT
*
1844285 TTTAGAC
192 TTTGGAC
* *
1844292 ----A-TATCGACACAAATTCCATAAGTGTCTG-TACATTATGTAGACCTATTCTCTCATAAAAC
1 AAAAAGTATCGACACAAATT-CAAAAGTGTC-GATACATTATGTAGACCTATTCTCACATAAAAC
* * * *
1844351 CGGTATAGTTATATCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTTGATGTT
64 CGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
* * * * * * *
1844416 TCTGGGATTGATATTTTTTATAAATGTATCGACACTTTATGTGTTCACCATTTTGGGATTCATTT
129 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCAGTTTGGCATTCATTT
1844481 TGGAC
194 TGGAC
* **
1844486 AAAAAGTATCGACACAAAATTCAAAAGTGTCGACACATTATGTAGACCTATTCTCACATAAAATT
1 AAAAAGTATCGACAC-AAATTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACC
* * ** *
1844551 GGTATATTTATACTGGTTATATTACAAAATTACCTATTACATTATAATTAT-GTGTTTCGATGTT
65 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCG-GTTTCGATGTT
* * * *
1844615 TTTGGGATCGATACTTTTTATAAATGTATCGATAATGTATGGGTGCACCACGTTTGGCATTCATT
129 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCA-GTTTGGCATTCATT
1844680 TTGGAC
193 TTGGAC
* * * ** * *
1844686 AAAAAGTATCGACACAAATTCCACAAGTTTCGATACATTATGTATATATATT-TTATCAAAAAAC
1 AAAAAGTATCGACACAAATT-CAAAAGTGTCGATACATTATGTAGACCTATTCTCA-CATAAAAC
* * *** * * *
1844750 CAGTATATTTATATCAACTACATTGTAAATTTACCTATTACATTATAATTTTTGGTTTCGATATT
64 CGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
* *
1844815 TTTGGGATCGATACTTTTTA-AACATGTATCAACAATTTATG
129 TTTGGGATCGATACTTTTTATAA-ATGTATCGACACTTTATG
1844856 GGAAACTTTA
Statistics
Matches: 639, Mismatches: 102, Indels: 44
0.81 0.13 0.06
Matches are distributed among these distances:
194 21 0.03
195 138 0.22
196 5 0.01
197 2 0.00
198 25 0.04
199 253 0.40
200 193 0.30
201 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (198 bp):
AAAAAGTATCGACACAAATTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCG
GTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
TGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCAGTTTGGCATTCATTTTG
GAC
Found at i:1844645 original size:394 final size:396
Alignment explanation
Indices: 1843897--1844855 Score: 1132
Period size: 394 Copynumber: 2.4 Consensus size: 396
1843887 GTTATTTAAA
* *
1843897 AAGTATCGACACAAATT-TAAAAGTGTCGATACATTATATTAACATATTCTCTCATAAAACCGGT
1 AAGTATCGACACAAATTCCAAAAGTGTCGATACATTAT-GTAACATATTCTCTCATAAAACCGGT
* * *
1843961 ATATTTATACCAGTTACATTGTAAATTTACATATTACGTTATAATTATCGGTTTCGATGTTTTTG
65 ATATTTATATCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTG
** * *
1844026 GGATCGATACAATTTAT-AATGTATCGACACTTTCTGCCTGCACCCCGTTTGACATTCATTCTGG
130 GGATCGATACTTTTTATAAATGTATCGACACTTTATGCCTGCACCCAGTTTGACATTCATTCTGG
* * * *
1844090 ACAAAATGTATCGACACAAATCTAAAACGTGTCGATACATTATGTTCACCTATTTTCTAATAAAA
195 ACAAAAAGTATCGACACAAATCTAAAACGTGTCGACACATTATGTACACCTATTCTCTAATAAAA
** * * *
1844155 CAAGTAAATTTATACCGGTTAAATTGTAAATTTACGTATTACATTATAATAATCGGTTTTGATGT
260 CAAGTAAATTTATACCGGTTAAATTACAAAATTACCTATTACATTATAATAATCGGTTTCGATGT
* * * * *
1844220 TTTTGGAATTGATACTTTTTAAAAATGTATCGATACTTTATGCGTGCAACC-CTTTTGGTATTCA
325 TTTTGGAATCGATACTTTTTAAAAATGTATCGATAATGTATGCGTGC-ACCACGTTTGGCATTCA
1844284 TTTTAGAC
389 TTTTAGAC
* *
1844292 -A-TATCGACACAAATTCCATAAGTGTCTG-TACATTATGTAGACCTATTCTCTCATAAAACCGG
1 AAGTATCGACACAAATTCCAAAAGTGTC-GATACATTATGTA-ACATATTCTCTCATAAAACCGG
* * * * *
1844354 TATAGTTATATCGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTTGATGTTTCT
64 TATATTTATATCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTT
* * ** * * ** *
1844419 GGGATTGATATTTTTTATAAATGTATCGACACTTTATGTGTTCA-CCATTTTGGGATTCATTTTG
129 GGGATCGATACTTTTTATAAATGTATCGACACTTTATGCCTGCACCCAGTTTGACATTCATTCTG
*
1844483 GACAAAAAGTATCGACACAAAAT-TCAAAA-GTGTCGACACATTATGTAGACCTATTCTC-ACAT
194 GACAAAAAGTATCGACAC-AAATCT-AAAACGTGTCGACACATTATGTACACCTATTCTCTA-AT
*** * * * *
1844545 AAAATTGGTATATTTATACTGGTTATATTACAAAATTACCTATTACATTATAATTAT-GTGTTTC
256 AAAACAAGTAAATTTATACCGGTTAAATTACAAAATTACCTATTACATTATAATAATCG-GTTTC
* * *
1844609 GATGTTTTTGGGATCGATACTTTTTATAAATGTATCGATAATGTATGGGTGCACCACGTTTGGCA
320 GATGTTTTTGGAATCGATACTTTTTAAAAATGTATCGATAATGTATGCGTGCACCACGTTTGGCA
*
1844674 TTCATTTTGGAC
385 TTCATTTTAGAC
* * * * * *
1844686 AAAAAGTATCGACACAAATTCCACAAGTTTCGATACATTATGTATATATATTTTATCAAAAAACC
1 ---AAGTATCGACACAAATTCCAAAAGTGTCGATACATTATGTA-ACATATTCTCTCATAAAACC
* ** * * *
1844751 AGTATATTTATATCAACTACATTGTAAATTTACCTATTACATTATAATTTTTGGTTTCGATATTT
62 GGTATATTTATATCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* *
1844816 TTGGGATCGATACTTTTTA-AACATGTATCAACAATTTATG
127 TTGGGATCGATACTTTTTATAA-ATGTATCGACACTTTATG
1844856 GGAAACTTTA
Statistics
Matches: 475, Mismatches: 73, Indels: 28
0.82 0.13 0.05
Matches are distributed among these distances:
393 21 0.04
394 283 0.60
395 30 0.06
398 4 0.01
399 137 0.29
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (396 bp):
AAGTATCGACACAAATTCCAAAAGTGTCGATACATTATGTAACATATTCTCTCATAAAACCGGTA
TATTTATATCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGG
GATCGATACTTTTTATAAATGTATCGACACTTTATGCCTGCACCCAGTTTGACATTCATTCTGGA
CAAAAAGTATCGACACAAATCTAAAACGTGTCGACACATTATGTACACCTATTCTCTAATAAAAC
AAGTAAATTTATACCGGTTAAATTACAAAATTACCTATTACATTATAATAATCGGTTTCGATGTT
TTTGGAATCGATACTTTTTAAAAATGTATCGATAATGTATGCGTGCACCACGTTTGGCATTCATT
TTAGAC
Found at i:1848483 original size:202 final size:198
Alignment explanation
Indices: 1847999--1849140 Score: 983
Period size: 199 Copynumber: 5.8 Consensus size: 198
1847989 CGAGATTTTT
* * * * * *
1847999 AAAATGGTATCGACACAAATTTAACAATTATCGATACTTTATGCT-GACCTATTTTCTCATAAAA
1 AAAAT-GTATCGACACAAA-TTAAAAAATGTCGATACATTATG-TAGACCTATTCTCACATAAAA
* * ****
1848063 CCGATATATTTATACCGGTTACATTGGAAATTTACCTATTACATTATAATTACCAATTTCGATAT
63 CCGATATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATAT
* *
1848128 TTTTGGGATCGATACTTTTTAAAAATATATCAACACTTAATGGGTGCACCCTTTTTACATTCCTT
128 TTATGGGATCGATACTTTTTAAAAATATATCAACACTTAATGGGTGCACCCTTTTTACATTACTT
1848193 CTGGAC
193 CTGGAC
* * * * * * * * * ** *
1848199 AAAAAGTATCGAAACAAATTCCAGAAGTGTCGATATATTTTCTAGACATATTCTTGCATAAAACT
1 AAAATGTATCGACACAAATT-AAAAAATGTCGATACATTATGTAGACCTATTCTCACATAAAACC
* * * *
1848264 GGTATATTTATACCGGTTAAATTGAAAAATTACCTATTACATTGTAATCATGGGTTTCGATATTT
65 GATATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATATTT
* * * * * * *
1848329 ATGGGATCGATACTTTTTATAAATGTATCGACACTTTATGTGTGCACCATTTTTTGGGCATTTAC
130 ATGGGATCGATACTTTTTAAAAATATATCAACACTTAATGGGTGCACC-CTTTTT--ACA-TTAC
1848394 -TCTGGAC
191 TTCTGGAC
*
1848401 AAAATGTATCGACACATAATTAAAAAATGTCGATACATTATGTAGACCTATTCACACATAAAACC
1 AAAATGTATCGACACA-AATTAAAAAATGTCGATACATTATGTAGACCTATTCTCACATAAAACC
* * *
1848466 GATATATTTATACCGGTTACATT-ACAAAATTTCCTATTACATTATAATTATGGG-TTCGATGTC
65 GATATATTTATACCGGTTACATTGA-AAAATTACCTATTACATTATAATTATGGGTTTCGATATT
* **** * *
1848529 TATGGGATCGACAC--TTT--ATGCGT-TCACCA-TT--TTGG-GCA------TT-C---A-TTC
129 TATGGGATCGATACTTTTTAAAAATATATCAACACTTAATGGGTGCACCCTTTTTACATTACTTC
1848574 TGGAC
194 TGGAC
* * * ** * *
1848579 AAAAAGTATCGACACCAATTTCAAATGTGTCGATACATTATGTAGACCTATTCTCATATAAAATC
1 AAAATGTATCGACA-CAAATTAAAAAATGTCGATACATTATGTAGACCTATTCTCACATAAAACC
* * *
1848644 GGTATATTTATACCGGTTACATT-ACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTC
65 GATATATTTATACCGGTTACATTGA-AAAATTACCTATTACATTATAATTATGGGTTTCGATATT
* * * * * * ** ** *
1848708 TCTGGGATCGACACTTTTAAAAAATGTATCGACACTTTATTTGTGCACCCTTTTGGGCATTCCTT
129 TATGGGATCGATACTTTTTAAAAATATATCAACACTTAATGGGTGCACCCTTTT-TACATTACTT
1848773 CTGGAC
193 CTGGAC
* * * * * * * *
1848779 AAACA-ATATCGACATAAATTCCATAAGTTTCGATACATTATGTAGACTTATTCTCTCATAAAAC
1 AAA-ATGTATCGACACAAATT-AAAAAATGTCGATACATTATGTAGACCTATTCTCACATAAAAC
* * * *
1848843 CGGTATAGTTT-TATCGGTTACGTTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGT
64 CGATATA-TTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATAT
* * * * * * * * ***
1848907 TTCTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCATTTTGGGATT-CAT
128 TTATGGGATCGATACTTTTTAAAAATATATCAACACTTAATGGGTGCACCCTTTTTACATTAC-T
* *
1848971 TTTAGAC
192 TCTGGAC
* * *
1848978 AAAAAGTATCGACACAAATTTAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCG
1 AAAATGTATCGACACAAATTAAAAAATGTCGATACATTATGTAGACCTATTCTCACATAAAACCG
* * *
1849043 GTATATTTATACCGGTTATATT-ACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
66 ATATATTTATACCGGTTACATTGA-AAAATTACCTATTACATTATAATTATGGGTTTCGATATTT
* * * *
1849107 TTGGGATCGATACTTTTTATAAATGTATCGACAC
130 ATGGGATCGATACTTTTTAAAAATATATCAACAC
1849141 ATCTGCTTAC
Statistics
Matches: 786, Mismatches: 116, Indels: 82
0.80 0.12 0.08
Matches are distributed among these distances:
178 114 0.15
179 24 0.03
181 2 0.00
182 1 0.00
183 3 0.00
184 4 0.01
185 4 0.01
187 3 0.00
188 3 0.00
192 3 0.00
193 2 0.00
194 1 0.00
195 2 0.00
196 5 0.01
197 7 0.01
198 133 0.17
199 172 0.22
200 167 0.21
201 26 0.03
202 103 0.13
203 7 0.01
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.37
Consensus pattern (198 bp):
AAAATGTATCGACACAAATTAAAAAATGTCGATACATTATGTAGACCTATTCTCACATAAAACCG
ATATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATATTTA
TGGGATCGATACTTTTTAAAAATATATCAACACTTAATGGGTGCACCCTTTTTACATTACTTCTG
GAC
Found at i:1848656 original size:178 final size:180
Alignment explanation
Indices: 1848355--1849122 Score: 573
Period size: 178 Copynumber: 4.1 Consensus size: 180
1848345 TTATAAATGT
* * *
1848355 ATCGACACTTTATGTGTGCACCATTTTTTGGGCATTTACTCTGGACAAAATGTATCGACACATAA
1 ATCGACACTTTATGCGTGCACCA-TTTTTGGGCATTCACTCTGGACAAAAAGTATCGACACATAA
1848420 TTAAAAAATGTCGATACATTATGTAGACCTATTCACACATAAAACCGATATATTTATACCGGTTA
65 TTAAAAAATGTCGATACATTATGTAGACCTATTCACACATAAAACCGATATATTTATACCGGTTA
*
1848485 CATTACAAAATTTCCTATTACATTATAATTATGGG-TTCGATGTCTATGGG
130 CATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCTATGGG
* * *
1848535 ATCGACACTTTATGCGTTCACCA-TTTTGGGCATTCATTCTGGACAAAAAGTATCGACACCA-AT
1 ATCGACACTTTATGCGTGCACCATTTTTGGGCATTCACTCTGGACAAAAAGTATCGACA-CATAA
* ** * * * *
1848598 TTCAAATGTGTCGATACATTATGTAGACCTATTCTCATATAAAATCGGTATATTTATACCGGTTA
65 TTAAAAAATGTCGATACATTATGTAGACCTATTCACACATAAAACCGATATATTTATACCGGTTA
*
1848663 CATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCTCTGGG
130 CATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCTATGGG
** * * * ****
1848714 ATCGACACTTTTAAAAAATGTAT-CGACACTTTATTTGTGCACCCTTTTGGGCATTCCTTCTGGA
1 ATCGACAC-TTT-----ATGCGTGC-AC-CATT-TTTGGGCA-----TT---CACT-C-TGGACA
* * * * * * * * * *
1848778 CAAACAATATCGACATA-AATTCCATAAGTTTCGATACATTATGTAGACTTATTCTCTCATAAAA
47 AA-A-AGTATCGACACATAATT-AAAAAATGTCGATACATTATGTAGACCTATTCACACATAAAA
* * *
1848842 CCGGTATAGTTT-TATCGGTTACGTTGA-AAAATTACCTATTACATTATAATTATGGGTTTCGAT
109 CCGATATA-TTTATACCGGTTACATT-ACAAAATTACCTATTACATTATAATTATGGGTTTCGAT
* *
1848905 GTTTCTGGG
172 GTCTATGGG
* ** * * * *
1848914 ATCGATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCATTTTGGG-ATTCATTTTAGAC
1 ATCGACAC---TT-T--ATG---CG--------TGC-ACCAT--TTTTGGGCATTCACTCTGGAC
* * *
1848978 AAAAAGTATCGACACA-AATTTAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACC
46 AAAAAGTATCGACACATAATTAAAAAATGTCGATACATTATGTAGACCTATTCACACATAAAACC
* * *
1849042 GGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
111 GATATATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCT
*
1849107 TTGGG
176 ATGGG
*
1849112 ATCGATACTTT
1 ATCGACACTTT
1849123 TTATAAATGT
Statistics
Matches: 480, Mismatches: 62, Indels: 78
0.77 0.10 0.13
Matches are distributed among these distances:
178 125 0.26
179 24 0.05
180 24 0.05
184 1 0.00
185 6 0.01
186 1 0.00
187 1 0.00
188 7 0.01
193 2 0.00
194 1 0.00
195 2 0.00
196 4 0.01
197 5 0.01
198 110 0.23
199 19 0.04
200 120 0.25
201 7 0.01
202 3 0.01
203 5 0.01
206 2 0.00
211 3 0.01
212 7 0.01
213 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.37
Consensus pattern (180 bp):
ATCGACACTTTATGCGTGCACCATTTTTGGGCATTCACTCTGGACAAAAAGTATCGACACATAAT
TAAAAAATGTCGATACATTATGTAGACCTATTCACACATAAAACCGATATATTTATACCGGTTAC
ATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCTATGGG
Found at i:1849101 original size:198 final size:199
Alignment explanation
Indices: 1848535--1849140 Score: 914
Period size: 200 Copynumber: 3.0 Consensus size: 199
1848525 TGTCTATGGG
*
1848535 ATCGACACTTTATGCGTTCACCATTTTGGGCATTCATTCTGGACAAAAAGTATCGACACCAATTT
1 ATCGACACTTTATGCGTTCACCATTTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAATTT
* * *
1848600 CAAATGTGTCGATACATTATGTAGACCTATTCTCATATAAAATCGGTATATTTATACCGGTTACA
66 -AAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCGGTTACA
* * * *
1848665 TTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCTCTGGGATCGACACTTTTAAAA
130 TTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGGATCGATACTTTTTATA
1848730 AATGT
195 AATGT
** * * * *
1848735 ATCGACACTTTATTTGTGCACCCTTTTGGGCATTCCTTCTGGACAAACAA-TATCGACATAAATT
1 ATCGACACTTTATGCGTTCACCATTTTGGGCATTCATTCTGGACAAA-AAGTATCGACACAAATT
* * * * * *
1848799 CCATAAGTTTCGATACATTATGTAGACTTATTCTCTCATAAAACCGGTATAGTTT-TATCGGTTA
65 -TAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATA-TTTATACCGGTTA
*
1848863 CGTTGA-AAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGGATCGATACTTTTT
128 CATT-ACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGGATCGATACTTTTT
1848927 ATAAATGT
192 ATAAATGT
* *
1848935 ATCGACACTTTATGCGTTCACCATTTTGGG-ATTCATTTTAGACAAAAAGTATCGACACAAATTT
1 ATCGACACTTTATGCGTTCACCATTTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAATTT
*
1848999 AAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCGGTTATAT
66 AAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCGGTTACAT
*
1849064 TACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGATACTTTTTATAA
131 TACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGGATCGATACTTTTTATAA
1849129 ATGT
196 ATGT
1849133 ATCGACAC
1 ATCGACAC
1849141 ATCTGCTTAC
Statistics
Matches: 361, Mismatches: 38, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
197 4 0.01
198 130 0.36
199 26 0.07
200 195 0.54
201 6 0.02
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (199 bp):
ATCGACACTTTATGCGTTCACCATTTTGGGCATTCATTCTGGACAAAAAGTATCGACACAAATTT
AAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGGTATATTTATACCGGTTACAT
TACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGGATCGATACTTTTTATAA
ATGT
Found at i:1851012 original size:18 final size:18
Alignment explanation
Indices: 1850989--1851045 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 18
1850979 TCCTCATTAT
1850989 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
* *
1851007 TTCCTCCGTATTTTCTTC
1 TTCCTCCATCTTTTCTTC
*
1851025 TTCCTCCATCTTTTATTC
1 TTCCTCCATCTTTTCTTC
1851043 TTC
1 TTC
1851046 ATATTTTTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.07, C:0.35, G:0.02, T:0.56
Consensus pattern (18 bp):
TTCCTCCATCTTTTCTTC
Found at i:1851244 original size:21 final size:21
Alignment explanation
Indices: 1851220--1851285 Score: 123
Period size: 21 Copynumber: 3.1 Consensus size: 21
1851210 CCATCTTAAG
1851220 TTCACCCCTCAACACCTCAAC
1 TTCACCCCTCAACACCTCAAC
1851241 TTCACCCCTCAACACCTCAAC
1 TTCACCCCTCAACACCTCAAC
*
1851262 TTCACCCCTTAACACCTCAAC
1 TTCACCCCTCAACACCTCAAC
1851283 TTC
1 TTC
1851286 TTTCACCACT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.27, C:0.50, G:0.00, T:0.23
Consensus pattern (21 bp):
TTCACCCCTCAACACCTCAAC
Found at i:1851381 original size:21 final size:21
Alignment explanation
Indices: 1851329--1851372 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1851319 CCTCTTATGC
*
1851329 CTCTCAAGTGTCTCTTCGACT
1 CTCTCAAGTCTCTCTTCGACT
1851350 CTCTCAAGTCTCTCTTCGACT
1 CTCTCAAGTCTCTCTTCGACT
1851371 CT
1 CT
1851373 TGATTGTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.36, G:0.11, T:0.39
Consensus pattern (21 bp):
CTCTCAAGTCTCTCTTCGACT
Found at i:1854381 original size:182 final size:182
Alignment explanation
Indices: 1853788--1854356 Score: 931
Period size: 182 Copynumber: 3.1 Consensus size: 182
1853778 CGTACTTAAT
* * * * * * * * *
1853788 AAGTATCGACACTTTAAATATATCCGGTAGCACTTTACCGATTTTGTCATTTCGAGACCGGTTTT
1 AAGTATCGACACTTTAAATATATTCGGTCGCTCTATACCGGTTTTGTCCTTTAGAAACCGATTTT
* * * *
1853853 GTCATATTTTTACATGTTATATCGTTGTGGACCGATACATTGTTATAAAGTATCGACACTTTATA
66 GTCATATTTTTACTTGTTATATCGTTTTGGATCGATACATTGTTATAAAGTATCGACACTTTATG
1853918 GGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTA
131 GGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTA
1853970 AAGTATCGACACTTTAAATATATTCGGTCGCTCTATACCGGTTTTGTCCTTTAGAAACCGATTTT
1 AAGTATCGACACTTTAAATATATTCGGTCGCTCTATACCGGTTTTGTCCTTTAGAAACCGATTTT
* *
1854035 GTCATATTTTTACTTGTTATATCGTTTTGGATCGATACATTATTATAAAGTATCGACGCTTTATG
66 GTCATATTTTTACTTGTTATATCGTTTTGGATCGATACATTGTTATAAAGTATCGACACTTTATG
* **
1854100 AGCGCTAAAACTGCTTCTCTTTTAAATTCACAATCTGTCGATACTTATATTA
131 GGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTA
*
1854152 AAGTATCGACACTTTCAATATATTCGGTCGCTCTATACCGGTTTTGTCCTTTAGAAACCGATTTT
1 AAGTATCGACACTTTAAATATATTCGGTCGCTCTATACCGGTTTTGTCCTTTAGAAACCGATTTT
*
1854217 GTCATATTTTTACTTGTTATATCGTTTTGGATTGATACATTGTTATAAAGTATCGACACTTTATG
66 GTCATATTTTTACTTGTTATATCGTTTTGGATCGATACATTGTTATAAAGTATCGACACTTTATG
* *
1854282 GGCGCTAAAACCGCTTCTCTTTTAAATTCACAAAGTGTCGATTCTTATATTA
131 GGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTA
*
1854334 AAGTATCGACACTTTCAATATAT
1 AAGTATCGACACTTTAAATATAT
1854357 CTGGTATCGC
Statistics
Matches: 360, Mismatches: 27, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
182 360 1.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (182 bp):
AAGTATCGACACTTTAAATATATTCGGTCGCTCTATACCGGTTTTGTCCTTTAGAAACCGATTTT
GTCATATTTTTACTTGTTATATCGTTTTGGATCGATACATTGTTATAAAGTATCGACACTTTATG
GGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTA
Found at i:1856516 original size:29 final size:29
Alignment explanation
Indices: 1856479--1856567 Score: 97
Period size: 29 Copynumber: 3.1 Consensus size: 29
1856469 CCCCAACACC
*
1856479 CCTACAAGGTCGCCAACCACTCCCAGTGA
1 CCTACAAGGTCGCCAACCACTCCCAGCGA
**
1856508 CCTACAAGGTCGCCATGCACTCCCAGCGA
1 CCTACAAGGTCGCCAACCACTCCCAGCGA
*** * * *
1856537 CCTTGTAGGTCGCCAAGCAATCCCGGCGA
1 CCTACAAGGTCGCCAACCACTCCCAGCGA
1856566 CC
1 CC
1856568 AAGCTTCACG
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.24, C:0.40, G:0.21, T:0.15
Consensus pattern (29 bp):
CCTACAAGGTCGCCAACCACTCCCAGCGA
Found at i:1856850 original size:26 final size:26
Alignment explanation
Indices: 1856817--1856874 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
1856807 ACATAAAAGA
*
1856817 AAGAAAGGGAGAAGAGATTGCAGCAG
1 AAGAAAGGGAGAAGAAATTGCAGCAG
*
1856843 AAGAAAGGGAGAAGAAATTGCAGCCG
1 AAGAAAGGGAGAAGAAATTGCAGCAG
1856869 -AGAAAG
1 AAGAAAG
1856875 AAAGAAAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 6 0.20
26 24 0.80
ACGTcount: A:0.48, C:0.09, G:0.36, T:0.07
Consensus pattern (26 bp):
AAGAAAGGGAGAAGAAATTGCAGCAG
Found at i:1857040 original size:22 final size:21
Alignment explanation
Indices: 1857015--1857055 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1857005 GTTAATTAGT
*
1857015 TTGTTAATTTAGGGTTATATGA
1 TTGTTAATTTA-AGTTATATGA
*
1857037 TTGTTAGTTTAAGTTATAT
1 TTGTTAATTTAAGTTATAT
1857056 TATACATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.54
Consensus pattern (21 bp):
TTGTTAATTTAAGTTATATGA
Found at i:1857111 original size:39 final size:39
Alignment explanation
Indices: 1857068--1857190 Score: 108
Period size: 39 Copynumber: 3.1 Consensus size: 39
1857058 TACATAAATA
*
1857068 AAAAATTATTTAATTAGTATGTTTGATAGTTATATAGTT
1 AAAAATTATTTAATTAGTTTGTTTGATAGTTATATAGTT
* * * *
1857107 AAAAAATAATTAATTAGTTTGTTTTGTTAATCGTTAGTTATA-TAA
1 AAAAATTATTTAATTAGTTTG-TTTG---ATAGTTA--TATAGT-T
*
1857152 AAAAATTATTTAATTAGTTTG-TTG-TAGTTAAATAGTT
1 AAAAATTATTTAATTAGTTTGTTTGATAGTTATATAGTT
1857189 AA
1 AA
1857191 GTTATATTTG
Statistics
Matches: 66, Mismatches: 10, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
37 5 0.08
38 1 0.02
39 23 0.35
40 4 0.06
43 9 0.14
44 1 0.02
45 23 0.35
ACGTcount: A:0.40, C:0.01, G:0.12, T:0.47
Consensus pattern (39 bp):
AAAAATTATTTAATTAGTTTGTTTGATAGTTATATAGTT
Found at i:1857169 original size:45 final size:47
Alignment explanation
Indices: 1857107--1857197 Score: 125
Period size: 45 Copynumber: 2.0 Consensus size: 47
1857097 TTATATAGTT
* *
1857107 AAAAAATAATTAATTAGTTTGTT-TTGTT-AATCGTT-AGTTATATA
1 AAAAAATAATTAATTAGTTTGTTGTAGTTAAATAGTTAAGTTATATA
*
1857151 AAAAAATTATTTAATTAGTTTGTTGTAGTTAAATAGTTAAGTTATAT
1 AAAAAA-TAATTAATTAGTTTGTTGTAGTTAAATAGTTAAGTTATAT
1857198 TTGTTTGTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
44 6 0.15
45 16 0.40
46 4 0.10
47 6 0.15
48 8 0.20
ACGTcount: A:0.40, C:0.01, G:0.12, T:0.47
Consensus pattern (47 bp):
AAAAAATAATTAATTAGTTTGTTGTAGTTAAATAGTTAAGTTATATA
Found at i:1859622 original size:14 final size:14
Alignment explanation
Indices: 1859603--1859650 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
1859593 TTCAAGTCGT
1859603 AAATCATTACTATC
1 AAATCATTACTATC
1859617 AAATCATTAC--T-
1 AAATCATTACTATC
*
1859628 AAATCATTAATATC
1 AAATCATTACTATC
1859642 AAATCATTA
1 AAATCATTA
1859651 AATATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 9 0.30
12 1 0.03
13 1 0.03
14 19 0.63
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:1859630 original size:25 final size:25
Alignment explanation
Indices: 1859602--1859650 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
1859592 GTTCAAGTCG
*
1859602 TAAATCATTACTATCAAATCATTAC
1 TAAATCATTAATATCAAATCATTAC
1859627 TAAATCATTAATATCAAATCATTA
1 TAAATCATTAATATCAAATCATTA
1859651 AATATTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (25 bp):
TAAATCATTAATATCAAATCATTAC
Found at i:1859666 original size:21 final size:22
Alignment explanation
Indices: 1859602--1859660 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 22
1859592 GTTCAAGTCG
*
1859602 TAAATCATTACTATCAAATCATT
1 TAAATCATTAATATCAAATCA-T
1859625 ACTAAATCATTAATATCAAATCAT
1 --TAAATCATTAATATCAAATCAT
1859649 TAAAT-ATTAATA
1 TAAATCATTAATA
1859661 ATAAATTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
21 7 0.21
22 5 0.15
24 1 0.03
25 20 0.61
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAATCATTAATATCAAATCAT
Found at i:1859671 original size:21 final size:22
Alignment explanation
Indices: 1859602--1859671 Score: 63
Period size: 21 Copynumber: 3.1 Consensus size: 22
1859592 GTTCAAGTCG
* *
1859602 TAAATCATTACTATCAAATCATTAC
1 TAAATCATTAATATC-AA--ATTAT
*
1859627 TAAATCATTAATATCAAATCAT
1 TAAATCATTAATATCAAATTAT
1859649 TAAAT-ATTAATAAT-AAATTAT
1 TAAATCATTAAT-ATCAAATTAT
1859670 TA
1 TA
1859672 TTACTAATCA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 14 0.35
22 10 0.25
24 2 0.05
25 14 0.35
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATCATTAATATCAAATTAT
Found at i:1859683 original size:59 final size:60
Alignment explanation
Indices: 1859618--1859865 Score: 430
Period size: 59 Copynumber: 4.2 Consensus size: 60
1859608 ATTACTATCA
* *
1859618 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATT-ATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
*
1859677 AATCATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
*
1859736 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
*
1859796 AATCATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
1859855 AATCATTACTA
1 AATCATTACTA
1859866 TCAAATCATT
Statistics
Matches: 179, Mismatches: 7, Indels: 5
0.94 0.04 0.03
Matches are distributed among these distances:
58 36 0.20
59 86 0.48
60 57 0.32
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (60 bp):
AATCATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
Found at i:1859686 original size:10 final size:10
Alignment explanation
Indices: 1859671--1859816 Score: 56
Period size: 10 Copynumber: 14.7 Consensus size: 10
1859661 ATAAATTATT
1859671 ATTACTAATC
1 ATTACTAATC
1859681 ATTACTAATC
1 ATTACTAATC
1859691 ATTACT-ATC
1 ATTACTAATC
* * **
1859700 AAATCATTAAAA
1 --ATTACTAATC
* *
1859712 ATTAATAATA
1 ATTACTAATC
* *
1859722 ATT--TCATT
1 ATTACTAATC
1859730 ATTACTAATC
1 ATTACTAATC
1859740 ATTACTAAATC
1 ATTACT-AATC
*
1859751 ATTAATATCAAATC
1 A-T--TA-CTAATC
1859765 ATTA--AAT-
1 ATTACTAATC
* *
1859772 ATTAATAATA
1 ATTACTAATC
* *
1859782 ATT--TCATT
1 ATTACTAATC
1859790 ATTACTAATC
1 ATTACTAATC
1859800 ATTACTAATC
1 ATTACTAATC
1859810 ATTACTA
1 ATTACTA
1859817 TCAAATCATT
Statistics
Matches: 105, Mismatches: 16, Indels: 30
0.70 0.11 0.20
Matches are distributed among these distances:
7 4 0.04
8 15 0.14
9 6 0.06
10 58 0.55
11 11 0.10
12 2 0.02
13 1 0.01
14 7 0.07
15 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTACTAATC
Found at i:1859744 original size:49 final size:49
Alignment explanation
Indices: 1859681--1860278 Score: 703
Period size: 49 Copynumber: 11.3 Consensus size: 49
1859671 ATTACTAATC
1859681 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
* *
1859730 ATTACTAATCATTACTAAATCATTAAT-ATCAAATCATTAAATATTAATAATAATTTCATTATTA
1 ATTACTAATCATTACT--ATCA--AATCATTAAA-AATT--A-A-TAA---TAATTTC---A-T-
1859794 CTAAT
49 ----T
1859799 CATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 -ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1859849 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1859898 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
*
1859947 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAGT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTC------A-T--T
*
1860005 CATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAAT
1 -ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTC------A-T--T
1860065 CATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 -ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
* *
1860115 ATTACTAATTATTAATATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
* * *
1860164 ATTACTAATCATTAATATCAAATAATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
* *
1860213 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATC
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1860262 ATTACTAATCATTACTA
1 ATTACTAATCATTACTA
1860279 AATCTTATAA
Statistics
Matches: 500, Mismatches: 15, Indels: 68
0.86 0.03 0.12
Matches are distributed among these distances:
49 315 0.63
50 2 0.00
51 4 0.01
52 6 0.01
53 7 0.01
55 3 0.01
56 3 0.01
57 3 0.01
58 1 0.00
59 52 0.10
60 65 0.13
62 3 0.01
63 2 0.00
64 2 0.00
66 6 0.01
67 5 0.01
68 4 0.01
69 1 0.00
70 16 0.03
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
Found at i:1859993 original size:266 final size:266
Alignment explanation
Indices: 1859622--1860282 Score: 1142
Period size: 266 Copynumber: 2.4 Consensus size: 266
1859612 CTATCAAATC
*
1859622 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATTATTACTAATCATTACT
1 ATTACT-AATCATTAATATCAAATCATTAAATATTAATAAT--A--A-T-TT-C--ATTATTACT
*
1859687 AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
56 AATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCA
1859752 TTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAATCATTACTA
121 TTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAATCATTACTA
*
1859817 TCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTATCAAATCATTAAAAAT
186 TCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAATATCAAATCATTAAAAAT
1859882 TAATAATAATTTCATT
251 TAATAATAATTTCATT
* *
1859898 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
1 ATTACTAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACT
* *
1859963 ATCAAATCATTAAATATTAATAATAATTTCATTATTACTAGTCATTACTAAATCATTACTATCAA
66 ATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATCAA
1860028 ATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAATCATTACTATCAAATCATT
131 ATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAATCATTACTATCAAATCATT
*
1860093 AAAAATTAATAATAATTTCATTATTACTAATTATTAATATCAAATCATTAAAAATTAATAATAAT
196 AAAAATTAATAATAATTTCATTATTACTAATCATTAATATCAAATCATTAAAAATTAATAATAAT
1860158 TTCATT
261 TTCATT
*
1860164 ATTACTAATCATTAATATCAAATAATTAAATATTAATAATAATTTCATTATTACTAATCATTACT
1 ATTACTAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACT
*
1860229 ATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATCATTACTAAATC
66 ATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATC
1860283 TTATAAATAC
Statistics
Matches: 372, Mismatches: 13, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
266 328 0.88
268 1 0.00
269 2 0.01
270 1 0.00
271 1 0.00
273 1 0.00
275 32 0.09
276 6 0.02
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (266 bp):
ATTACTAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACT
ATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATCAA
ATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAATCATTACTATCAAATCATT
AAAAATTAATAATAATTTCATTATTACTAATCATTAATATCAAATCATTAAAAATTAATAATAAT
TTCATT
Found at i:1860041 original size:21 final size:20
Alignment explanation
Indices: 1859957--1860041 Score: 52
Period size: 21 Copynumber: 4.2 Consensus size: 20
1859947 ATTACTAATC
1859957 ATTACTATCAAATCATTAAAT
1 ATTACTATC-AATCATTAAAT
* * *
1859978 ATTA--AT-AATAATTTCATT
1 ATTACTATCAATCA-TTAAAT
* *
1859996 ATTACTAGTC-ATTACTAAAT
1 ATTACTA-TCAATCATTAAAT
1860016 CATTACTATCAAATCATTAAAT
1 -ATTACTATC-AATCATTAAAT
1860038 ATTA
1 ATTA
1860042 ATAATAATTT
Statistics
Matches: 47, Mismatches: 9, Indels: 16
0.65 0.12 0.22
Matches are distributed among these distances:
17 4 0.09
18 8 0.17
19 2 0.04
20 6 0.13
21 19 0.40
22 8 0.17
ACGTcount: A:0.45, C:0.13, G:0.01, T:0.41
Consensus pattern (20 bp):
ATTACTATCAATCATTAAAT
Found at i:1860071 original size:10 final size:10
Alignment explanation
Indices: 1860056--1860082 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1860046 TAATTTCATT
1860056 ATTACTAATC
1 ATTACTAATC
1860066 ATTACTAATC
1 ATTACTAATC
1860076 ATTACTA
1 ATTACTA
1860083 TCAAATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTACTAATC
Found at i:1860148 original size:24 final size:24
Alignment explanation
Indices: 1860081--1860155 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
1860071 TAATCATTAC
1860081 TATCAAATCATTAAAAATTAATAA
1 TATCAAATCATTAAAAATTAATAA
*** * ** *
1860105 TAATTTCATTATTACTAATTATTAA
1 T-ATCAAATCATTAAAAATTAATAA
1860130 TATCAAATCATTAAAAATTAATAA
1 TATCAAATCATTAAAAATTAATAA
1860154 TA
1 TA
1860156 ATTTCATTAT
Statistics
Matches: 36, Mismatches: 14, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
24 19 0.53
25 17 0.47
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (24 bp):
TATCAAATCATTAAAAATTAATAA
Found at i:1860172 original size:18 final size:17
Alignment explanation
Indices: 1860097--1860221 Score: 55
Period size: 18 Copynumber: 7.5 Consensus size: 17
1860087 ATCATTAAAA
* *
1860097 ATTAATAATAATTTCATT
1 ATTACTAATAA-TTCAAT
*
1860115 ATTACTAATTATT-AAT
1 ATTACTAATAATTCAAT
* * * *
1860131 A-T-CAAATCATTAAAA
1 ATTACTAATAATTCAAT
* *
1860146 ATTAATAATAATTTCATT
1 ATTACTAATAA-TTCAAT
*
1860164 ATTACTAATCATT-AAT
1 ATTACTAATAATTCAAT
* *
1860180 A-T-CAAATAATTAAAT
1 ATTACTAATAATTCAAT
* *
1860195 ATTAATAATAATTTCATT
1 ATTACTAATAA-TTCAAT
1860213 ATTACTAAT
1 ATTACTAAT
1860222 CATTACTATC
Statistics
Matches: 77, Mismatches: 22, Indels: 16
0.67 0.19 0.14
Matches are distributed among these distances:
14 14 0.18
15 9 0.12
16 8 0.10
17 13 0.17
18 33 0.43
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTACTAATAATTCAAT
Found at i:1863830 original size:28 final size:30
Alignment explanation
Indices: 1863789--1863850 Score: 110
Period size: 28 Copynumber: 2.1 Consensus size: 30
1863779 ATTTTTTATA
1863789 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
1863819 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
1863847 TAAT
1 TAAT
1863851 TAACTAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:1864304 original size:23 final size:23
Alignment explanation
Indices: 1864274--1864317 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1864264 GCTTGGCTAC
1864274 AATCTCCCAGCTATGGATGCAGG
1 AATCTCCCAGCTATGGATGCAGG
1864297 AATCTCCCAGCTATGGATGCA
1 AATCTCCCAGCTATGGATGCA
1864318 ACCCATGCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (23 bp):
AATCTCCCAGCTATGGATGCAGG
Found at i:1865516 original size:17 final size:18
Alignment explanation
Indices: 1865494--1865527 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1865484 TCGACTTTAA
*
1865494 CTTTTTA-CAATTTCTTT
1 CTTTTTATCAAGTTCTTT
1865511 CTTTTTATCAAGTTCTT
1 CTTTTTATCAAGTTCTT
1865528 AATCACTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.18, C:0.18, G:0.03, T:0.62
Consensus pattern (18 bp):
CTTTTTATCAAGTTCTTT
Found at i:1867189 original size:21 final size:21
Alignment explanation
Indices: 1867138--1867190 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
1867128 ATTATGACTA
* *
1867138 TCGCAATGCAATTTTCTAATT
1 TCGCAATGCGATTTTCCAATT
**
1867159 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
1867180 TCGCAATGCGA
1 TCGCAATGCGA
1867191 ATAAGTAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:1867222 original size:20 final size:20
Alignment explanation
Indices: 1867199--1867313 Score: 117
Period size: 20 Copynumber: 5.7 Consensus size: 20
1867189 GAATAAGTAA
*
1867199 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1867219 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
1867240 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1867260 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
1867280 TTCGCAACGAGATTA-TGACT
1 ATCGCAACGCGA-TACTGACT
*
1867300 ATCGCAACGAGATA
1 ATCGCAACGCGATA
1867314 ATACAGAATC
Statistics
Matches: 81, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
19 4 0.05
20 59 0.73
21 16 0.20
22 2 0.02
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1867242 original size:41 final size:41
Alignment explanation
Indices: 1867197--1867333 Score: 145
Period size: 41 Copynumber: 3.4 Consensus size: 41
1867187 GCGAATAAGT
*
1867197 AAATCGCAATGCGATACTGACTATCGCAACGCGATAATACA
1 AAATCGCAACGCGATACTGACTATCGCAACGCGATAATACA
* **
1867238 AAATCGCAACGCGATACTGACTTTCGCAACGCGATTCTGAC-
1 AAATCGCAACGCGATACTGACTATCGCAACGCGATAAT-ACA
** * *
1867279 -TTTCGCAACGAGATTA-TGACTATCGCAACGAGATAATACA
1 AAATCGCAACGCGA-TACTGACTATCGCAACGCGATAATACA
* *
1867319 GAATCGCAATGCGAT
1 AAATCGCAACGCGAT
1867334 TTTCAAAGTT
Statistics
Matches: 77, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
39 2 0.03
40 28 0.36
41 45 0.58
42 2 0.03
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (41 bp):
AAATCGCAACGCGATACTGACTATCGCAACGCGATAATACA
Found at i:1867954 original size:19 final size:19
Alignment explanation
Indices: 1867913--1867977 Score: 95
Period size: 19 Copynumber: 3.7 Consensus size: 19
1867903 GAAATGAAAA
1867913 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
1867929 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1867946 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1867965 TCGCATTGCGATT
1 TCGCATTGCGATT
1867978 CTCTCGTTGC
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
14 11 0.25
16 3 0.07
17 3 0.07
19 27 0.61
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1869602 original size:42 final size:42
Alignment explanation
Indices: 1869556--1869644 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
1869546 CCTCTTCAAT
* * * *
1869556 GATGACAGTGGCCTCTTGAACGGTGGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGGCGACTCTTGAGG
* * *
1869598 GATGATAGGGGCCTCTTGAATGATTGGAGGCGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGGCGACTCTTGAGG
1869640 GATGA
1 GATGA
1869645 TATGTGAGTC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.20, C:0.15, G:0.42, T:0.24
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGGCGACTCTTGAGG
Found at i:1869608 original size:21 final size:21
Alignment explanation
Indices: 1869584--1869646 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
1869574 AACGGTGGGG
1869584 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGATA
* ** *
1869605 GGGGCCTCTTGAATGATTG-GA
1 GGGGACTCTTGAGGGA-TGATA
*
1869626 GGCGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGATA
1869647 TGTGAGTCGG
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.22, C:0.13, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGATA
Found at i:1870035 original size:20 final size:20
Alignment explanation
Indices: 1870012--1870066 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
1870002 AAACTTACTT
1870012 TCGCAATGCGGAAATGGCTA
1 TCGCAATGCGGAAATGGCTA
*
1870032 TCGCAACGCGGAAATGGCTA
1 TCGCAATGCGGAAATGGCTA
1870052 TCGCAATGC-GAAATG
1 TCGCAATGCGGAAATG
1870067 AAAATCGCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 6 0.18
20 27 0.82
ACGTcount: A:0.31, C:0.22, G:0.29, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGGAAATGGCTA
Found at i:1870073 original size:19 final size:18
Alignment explanation
Indices: 1870051--1870109 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 18
1870041 GGAAATGGCT
1870051 ATCGCAATGCGAAATGAAA
1 ATCGCAAT-CGAAATGAAA
*
1870070 ATCGCAA-CG--A-CAAA
1 ATCGCAATCGAAATGAAA
1870084 ATCGCAATACGAAATGAAA
1 ATCGCAAT-CGAAATGAAA
1870103 ATCGCAA
1 ATCGCAA
1870110 CGACAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.49, C:0.20, G:0.17, T:0.14
Consensus pattern (18 bp):
ATCGCAATCGAAATGAAA
Found at i:1870086 original size:14 final size:14
Alignment explanation
Indices: 1870067--1870125 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
1870057 ATGCGAAATG
1870067 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1870081 AAAATCGCAATACGAAATG
1 AAAATCGC-A-ACG--A-C
1870100 AAAATCGCAACGAC
1 AAAATCGCAACGAC
1870114 AAAATCGCAACG
1 AAAATCGCAACG
1870126 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 20 0.53
15 2 0.05
16 3 0.08
17 3 0.08
18 2 0.05
19 8 0.21
ACGTcount: A:0.51, C:0.24, G:0.15, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1870141 original size:33 final size:33
Alignment explanation
Indices: 1870051--1870130 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
1870041 GGAAATGGCT
1870051 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1870084 ATCGCAATACGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1870117 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
1870131 CACAAATCGC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.49, C:0.23, G:0.17, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1870159 original size:19 final size:19
Alignment explanation
Indices: 1870137--1870219 Score: 95
Period size: 19 Copynumber: 4.6 Consensus size: 19
1870127 GAAACACAAA
1870137 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
1870156 TCGCGTTACGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
1870175 TCGCATTACGA-TTT--TG
1 TCGCATTGCGATTTTCATT
1870191 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1870208 TCGCATTGCGAT
1 TCGCATTGCGAT
1870220 AGCCATTTCC
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
14 5 0.09
15 3 0.06
16 4 0.08
17 4 0.08
18 3 0.06
19 34 0.64
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1870238 original size:20 final size:19
Alignment explanation
Indices: 1870204--1870258 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1870194 TTGCGATTTT
*
1870204 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1870223 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1870243 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
1870259 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1870816 original size:18 final size:18
Alignment explanation
Indices: 1870793--1870840 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1870783 CGGGTCGATC
1870793 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
1870811 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
1870829 AGGTGATGGCTC
1 AGGTGATGGCTC
1870841 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:1872208 original size:20 final size:20
Alignment explanation
Indices: 1872160--1872218 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1872150 AATAGTTTTT
* *
1872160 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
1872180 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
1872200 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
1872219 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:1872494 original size:22 final size:22
Alignment explanation
Indices: 1872467--1872510 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1872457 GATGGAGATA
*
1872467 GACGGATTTCGCCGGAGATGGG
1 GACGGATATCGCCGGAGATGGG
**
1872489 GACGGATATCGTTGGAGATGGG
1 GACGGATATCGCCGGAGATGGG
1872511 TGAGAGAGTG
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:0.20, C:0.14, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATATCGCCGGAGATGGG
Found at i:1872725 original size:20 final size:20
Alignment explanation
Indices: 1872697--1872768 Score: 117
Period size: 20 Copynumber: 3.6 Consensus size: 20
1872687 GATTATGTAT
*
1872697 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1872717 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
*
1872737 TATCGCATTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
1872757 TATCGCGTTGCG
1 TATCGCGTTGCG
1872769 GTTTTGTATT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1875198 original size:21 final size:21
Alignment explanation
Indices: 1875144--1875199 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
1875134 TGGGGAAAGA
*
1875144 GAGTATCAGTACTGATCAAGG
1 GAGTATCAGTATTGATCAAGG
*
1875165 GAGTATCGGTATTGATCAAGG
1 GAGTATCAGTATTGATCAAGG
*
1875186 GAGTATCAATATTG
1 GAGTATCAGTATTG
1875200 GTATTGATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.32, C:0.11, G:0.29, T:0.29
Consensus pattern (21 bp):
GAGTATCAGTATTGATCAAGG
Found at i:1875788 original size:2 final size:2
Alignment explanation
Indices: 1875783--1875817 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1875773 ATTAAAAAAT
1875783 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1875818 TGTGAAGATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1877325 original size:23 final size:23
Alignment explanation
Indices: 1877299--1877362 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
1877289 CAGCTCTTAT
1877299 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
1877322 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
1877345 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
1877363 TATAATAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:1877549 original size:103 final size:103
Alignment explanation
Indices: 1877382--1877587 Score: 349
Period size: 103 Copynumber: 2.0 Consensus size: 103
1877372 GTCCATAAGG
* * *
1877382 ACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTATCTCACCAGACT
*
1877447 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGA
66 TCACACATGTTCCAAAGAATACATATATGTCCCAAAGA
*
1877485 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTATCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTATCTCACCAGACT
* *
1877550 TTACACATGTTTCAAAGAATACATATATGTCCCAAAGA
66 TCACACATGTTCCAAAGAATACATATATGTCCCAAAGA
1877588 CCGCGTAGAC
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 96 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.28
Consensus pattern (103 bp):
ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTATCTCACCAGACT
TCACACATGTTCCAAAGAATACATATATGTCCCAAAGA
Found at i:1879922 original size:16 final size:16
Alignment explanation
Indices: 1879883--1879925 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1879873 AGCATCAGTT
*
1879883 CTTATCACTCAAAATC
1 CTTATCAATCAAAATC
* *
1879899 ATTAATCAATCAAATTC
1 CTT-ATCAATCAAAATC
1879916 CTTATCAATC
1 CTTATCAATC
1879926 TTTAATTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.35
Consensus pattern (16 bp):
CTTATCAATCAAAATC
Found at i:1882691 original size:23 final size:23
Alignment explanation
Indices: 1882665--1882728 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
1882655 CAGCTTTTAT
1882665 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
1882688 AATTGCACCTG-AGTGCCGCGTAG
1 AATTGCACC-GAAGTGCCACGTAG
*
1882711 AATTACACC-AGAGTGCCA
1 AATTGCACCGA-AGTGCCA
1882729 TATAATAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
23 34 0.97
24 1 0.03
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:1882915 original size:103 final size:103
Alignment explanation
Indices: 1882744--1882956 Score: 392
Period size: 103 Copynumber: 2.1 Consensus size: 103
1882734 TAATGTCCAT
*
1882744 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGTGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACAAGTGATCAAGTATGTGTCTCACCA
1882809 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1882847 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAG-GATCAAGTATGTGTCTCACC
1 AAGGACCACATATCATTCCTTAAGAATCATATACATAT-ACAAGTGATCAAGTATGTGTCTCACC
1882911 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
65 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1882950 AAGGACC
1 AAGGACC
1882957 GCGTAGACCC
Statistics
Matches: 107, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
103 104 0.97
104 3 0.03
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACAAGTGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1884369 original size:20 final size:21
Alignment explanation
Indices: 1884328--1884383 Score: 87
Period size: 20 Copynumber: 2.7 Consensus size: 21
1884318 TTCGCTTGAG
*
1884328 GGGTATCGATTCCCTATTGAAT
1 GGGTACCGATTCCC-ATTGAAT
1884350 GGGTACCGATTCCC-TTGAAT
1 GGGTACCGATTCCCATTGAAT
1884370 GGGTACCGATTCCC
1 GGGTACCGATTCCC
1884384 CTTGCCCAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
20 20 0.61
22 13 0.39
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.30
Consensus pattern (21 bp):
GGGTACCGATTCCCATTGAAT
Found at i:1887316 original size:27 final size:27
Alignment explanation
Indices: 1887241--1887318 Score: 102
Period size: 29 Copynumber: 2.8 Consensus size: 27
1887231 AAATTTTAAA
* * * *
1887241 ATTAAATGTTTATTTTTGTCTTAATTT
1 ATTAAATATTTATTTTTATTTTAATCT
1887268 ATTAAATATATTGATTTTTATTTTAATCT
1 ATTAAATAT-TT-ATTTTTATTTTAATCT
1887297 ATTAAATATTTATTTTTATTTT
1 ATTAAATATTTATTTTTATTTT
1887319 TATGTAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
27 19 0.42
28 4 0.09
29 22 0.49
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.63
Consensus pattern (27 bp):
ATTAAATATTTATTTTTATTTTAATCT
Found at i:1887346 original size:31 final size:28
Alignment explanation
Indices: 1887300--1887374 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 28
1887290 TTAATCTATT
*
1887300 AAATATTTATTTTTATTTTTA-TGTAAAAA
1 AAAT-TTTATTTTTATCTTTACT-TAAAAA
*
1887329 TATATATTTTATCTTTATCTTTACTTAAAAA
1 -A-A-ATTTTATTTTTATCTTTACTTAAAAA
1887360 AAATTTTATTTTTAT
1 AAATTTTATTTTTAT
1887375 ATTACTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
28 12 0.31
29 1 0.03
30 2 0.05
31 21 0.54
32 3 0.08
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.57
Consensus pattern (28 bp):
AAATTTTATTTTTATCTTTACTTAAAAA
Found at i:1888597 original size:18 final size:18
Alignment explanation
Indices: 1888574--1888610 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1888564 CATTTTTGGT
1888574 TGACAACCGAAAATGTTA
1 TGACAACCGAAAATGTTA
1888592 TGACAACCGAAAATGTTA
1 TGACAACCGAAAATGTTA
1888610 T
1 T
1888611 ATTTTTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.24
Consensus pattern (18 bp):
TGACAACCGAAAATGTTA
Found at i:1901125 original size:42 final size:43
Alignment explanation
Indices: 1901070--1901176 Score: 123
Period size: 42 Copynumber: 2.6 Consensus size: 43
1901060 GGTGATTCAT
* *
1901070 CGAGAAT-AGAAAGTGA-TATGCTTCCTTTCATTATACTTTAGA
1 CGAGAATCA-AAAGTGACGATGCCTCCTTTCATTATACTTTAGA
* *
1901112 CGAGAATCAAAAGT-ACGATGCCTCCTTTCGTTCTACTTTAGA
1 CGAGAATCAAAAGTGACGATGCCTCCTTTCATTATACTTTAGA
* *
1901154 CAAGAATCGAAAGTG-CGATGCCT
1 CGAGAATCAAAAGTGACGATGCCT
1901177 TTTTTGGTTC
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
41 1 0.02
42 54 0.96
43 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.30
Consensus pattern (43 bp):
CGAGAATCAAAAGTGACGATGCCTCCTTTCATTATACTTTAGA
Found at i:1901187 original size:42 final size:42
Alignment explanation
Indices: 1901087--1901191 Score: 129
Period size: 42 Copynumber: 2.5 Consensus size: 42
1901077 AGAAAGTGAT
* * * *
1901087 ATGCTTCCTTTCATTATACTTTAGACGAGAATCAAAAGTACG
1 ATGCCTCCTTTCGTTCTACTTTAGACAAGAATCAAAAGTACG
* *
1901129 ATGCCTCCTTTCGTTCTACTTTAGACAAGAATCGAAAGTGCG
1 ATGCCTCCTTTCGTTCTACTTTAGACAAGAATCAAAAGTACG
** *
1901171 ATGCCTTTTTTGGTTCTACTT
1 ATGCCTCCTTTCGTTCTACTT
1901192 ATTCACCTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (42 bp):
ATGCCTCCTTTCGTTCTACTTTAGACAAGAATCAAAAGTACG
Found at i:1913594 original size:19 final size:19
Alignment explanation
Indices: 1913570--1913607 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1913560 AATACTGGCC
*
1913570 TATGGGTTTCGATACTACT
1 TATGGGTATCGATACTACT
*
1913589 TATGGGTATCGATATTACT
1 TATGGGTATCGATACTACT
1913608 GACTTATTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.42
Consensus pattern (19 bp):
TATGGGTATCGATACTACT
Found at i:1915500 original size:109 final size:112
Alignment explanation
Indices: 1915360--1915575 Score: 275
Period size: 111 Copynumber: 2.0 Consensus size: 112
1915350 GATCGATATG
* *
1915360 TTCTATTACAATGCTGCTAGCATTGTATTCATCCA-ATCA-TCTCTGATTCAGTATTC-TCGGTA
1 TTCTATCACAATGCTGCTAGCATTGCATTCATCCATATCATTCTCTGATTCAGTATTCGTC-GTA
*
1915422 GAAGTTAG-TAGAAGAA-TAAGTGGAAGTAGAT-AATTACCTTGGGTATT
65 -AAGGTAGATAGAAGAAGT-AGTGGAAGTAGATGAATTACCTTGGGTATT
* * * *
1915469 TTCTATCACAATGC-GACTAGCATTGCATTCATCGATGTCATTGTCTGATTTAGTATTCGTCGTA
1 TTCTATCACAATGCTG-CTAGCATTGCATTCATCCATATCATTCTCTGATTCAGTATTCGTCGTA
*
1915533 AAGGTGGATAGAAGAAGTAGTGGAAGTAGATGAATTACCTTGG
65 AAGGTAGATAGAAGAAGTAGTGGAAGTAGATGAATTACCTTGG
1915576 TAAGTAGATG
Statistics
Matches: 92, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
108 1 0.01
109 30 0.33
110 8 0.09
111 39 0.42
112 14 0.15
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (112 bp):
TTCTATCACAATGCTGCTAGCATTGCATTCATCCATATCATTCTCTGATTCAGTATTCGTCGTAA
AGGTAGATAGAAGAAGTAGTGGAAGTAGATGAATTACCTTGGGTATT
Found at i:1915580 original size:21 final size:21
Alignment explanation
Indices: 1915556--1915621 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
1915546 GAAGTAGTGG
*
1915556 AAGTAGATGAATTACCTTGGT
1 AAGTAGATGAAGTACCTTGGT
1915577 AAGTAGATGAAGTACCTTGGT
1 AAGTAGATGAAGTACCTTGGT
* *
1915598 AAATAGGT-AAGTACCTTGGT
1 AAGTAGATGAAGTACCTTGGT
1915618 AAGT
1 AAGT
1915622 GTCTCTGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 15 0.37
21 26 0.63
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.30
Consensus pattern (21 bp):
AAGTAGATGAAGTACCTTGGT
Found at i:1918071 original size:21 final size:21
Alignment explanation
Indices: 1918045--1918111 Score: 107
Period size: 21 Copynumber: 3.2 Consensus size: 21
1918035 GAAGTAGTGA
*
1918045 AAGTAGATGAATTACCTTGGT
1 AAGTAGATGAAGTACCTTGGT
1918066 AAGTAGATGAAGTACCTTGGT
1 AAGTAGATGAAGTACCTTGGT
* *
1918087 AAATAGATAAAGTACCTTGGT
1 AAGTAGATGAAGTACCTTGGT
1918108 AAGT
1 AAGT
1918112 GTCTCTGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.30
Consensus pattern (21 bp):
AAGTAGATGAAGTACCTTGGT
Found at i:1938994 original size:21 final size:21
Alignment explanation
Indices: 1938970--1939038 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
1938960 GAATCGATAC
1938970 CCCCTTGAAGGGGAACCGATT
1 CCCCTTGAAGGGGAACCGATT
1938991 CCCCCTTTGAAGGGGAACCGATT
1 -CCCC-TTGAAGGGGAACCGATT
* * * *
1939014 CCCCCTGTAGGGGAATCGATA
1 CCCCTTGAAGGGGAACCGATT
1939035 CCCC
1 CCCC
1939039 CCTGGGGTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
21 17 0.40
22 8 0.19
23 17 0.40
ACGTcount: A:0.22, C:0.33, G:0.26, T:0.19
Consensus pattern (21 bp):
CCCCTTGAAGGGGAACCGATT
Found at i:1939040 original size:23 final size:22
Alignment explanation
Indices: 1938958--1939039 Score: 103
Period size: 23 Copynumber: 3.7 Consensus size: 22
1938948 TTAGTATAGA
*
1938958 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCTTGAAG
*
1938980 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-TTGAAG
* *
1939003 GGGAACCGATTCCCCC-TGTAG
1 GGGAACCGATACCCCCTTGAAG
*
1939024 GGGAATCGATACCCCC
1 GGGAACCGATACCCCC
1939040 CTGGGGTTCT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
21 18 0.33
22 14 0.26
23 22 0.41
ACGTcount: A:0.23, C:0.32, G:0.27, T:0.18
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGAAG
Found at i:1939042 original size:22 final size:22
Alignment explanation
Indices: 1938958--1939042 Score: 91
Period size: 22 Copynumber: 3.9 Consensus size: 22
1938948 TTAGTATAGA
* *
1938958 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCCTGAAG
* *
1938980 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-CTGAAG
* *
1939003 GGGAACCGAT-TCCCCCTGTAG
1 GGGAACCGATACCCCCCTGAAG
*
1939024 GGGAATCGATACCCCCCTG
1 GGGAACCGATACCCCCCTG
1939043 GGGTTCTGGT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
21 13 0.24
22 25 0.46
23 16 0.30
ACGTcount: A:0.22, C:0.32, G:0.27, T:0.19
Consensus pattern (22 bp):
GGGAACCGATACCCCCCTGAAG
Found at i:1940599 original size:18 final size:18
Alignment explanation
Indices: 1940576--1940612 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1940566 CAGCACGAGC
1940576 AACAAGCACGAG-CAGAGG
1 AACAAGCAC-AGCCAGAGG
1940594 AACAAGCACAGCCAGAGG
1 AACAAGCACAGCCAGAGG
1940612 A
1 A
1940613 TCAAATGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.46, C:0.24, G:0.30, T:0.00
Consensus pattern (18 bp):
AACAAGCACAGCCAGAGG
Found at i:1942734 original size:23 final size:23
Alignment explanation
Indices: 1942701--1942756 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
1942691 ATGTTTATAG
1942701 GTTG-AAATCATGCTTGAATCAA
1 GTTGAAAATCATGCTTGAATCAA
1942723 GTTGAAAATCATGCTTGAATCAA
1 GTTGAAAATCATGCTTGAATCAA
*
1942746 GTTAAAAATCA
1 GTTGAAAATCA
1942757 AGCATAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 4 0.12
23 28 0.88
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.30
Consensus pattern (23 bp):
GTTGAAAATCATGCTTGAATCAA
Found at i:1951618 original size:284 final size:284
Alignment explanation
Indices: 1951108--1951680 Score: 1074
Period size: 284 Copynumber: 2.0 Consensus size: 284
1951098 TATTGTTCTC
1951108 GCATAAAGTAAGGATTGGTCCGATCAAATTAGTTGGAAACCCATTCTAAATATTTATTGCCTCGA
1 GCATAAAGTAAGGATTGGTCCGATCAAATTAGTTGGAAACCCATTCTAAATATTTATTGCCTCGA
* *
1951173 AACCCACTCAGCATCACTTTGGTTAAGCATTATTGTATAAATATCACCATGAGGTACCCTTATTA
66 AACCCACTAAGCACCACTTTGGTTAAGCATTATTGTATAAATATCACCATGAGGTACCCTTATTA
* *
1951238 ACCATAAGGCAAGCGTCTCGGCAAACCTTAAAGATAAGTGCCCATGCACGCAAATCACCATTAAG
131 ACCATAAGGCAAGCGTCTCGGCAAACCTTAAAGACAAGTACCCATGCACGCAAATCACCATTAAG
1951303 AACCTCAATGCAATGGTAAACAAACTAGTGCCTCTTACGCAAAAACAAAATGCACACCTCTGTGC
196 AACCTCAATGCAATGGTAAACAAACTAGTGCCTCTTACGCAAAAACAAAATGCACACCTCTGTGC
* *
1951368 TTTCGCAGAGTAAGCACCCCTTAT
261 TTTCGCAAAGCAAGCACCCCTTAT
1951392 GCATAAAGTAAGGATTGGTCCGATCAAATTAGTTGGAAACCCATTCTAAATATTTATTGCCTCGA
1 GCATAAAGTAAGGATTGGTCCGATCAAATTAGTTGGAAACCCATTCTAAATATTTATTGCCTCGA
1951457 AACCCACTAAGCACCACTTTGGTTAAGCATTATTGTATAAATATCACCATGAGGTACCCTTATTA
66 AACCCACTAAGCACCACTTTGGTTAAGCATTATTGTATAAATATCACCATGAGGTACCCTTATTA
*
1951522 ACCATAAGGCAAGCGTCTCGGCAAACCTTAAAGACAAGTACCCATGCACGTAAATCACCATTAAG
131 ACCATAAGGCAAGCGTCTCGGCAAACCTTAAAGACAAGTACCCATGCACGCAAATCACCATTAAG
*
1951587 AACCTCAATGCAATGGTAAACAAACTAGTGCCTCTTACGCAAAAACAAAATGCACACCTTTGTGC
196 AACCTCAATGCAATGGTAAACAAACTAGTGCCTCTTACGCAAAAACAAAATGCACACCTCTGTGC
1951652 TTTCGCAAAGCAAGCACCCCTTAT
261 TTTCGCAAAGCAAGCACCCCTTAT
1951676 GCATA
1 GCATA
1951681 TATCTGCAGT
Statistics
Matches: 281, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
284 281 1.00
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (284 bp):
GCATAAAGTAAGGATTGGTCCGATCAAATTAGTTGGAAACCCATTCTAAATATTTATTGCCTCGA
AACCCACTAAGCACCACTTTGGTTAAGCATTATTGTATAAATATCACCATGAGGTACCCTTATTA
ACCATAAGGCAAGCGTCTCGGCAAACCTTAAAGACAAGTACCCATGCACGCAAATCACCATTAAG
AACCTCAATGCAATGGTAAACAAACTAGTGCCTCTTACGCAAAAACAAAATGCACACCTCTGTGC
TTTCGCAAAGCAAGCACCCCTTAT
Found at i:1965963 original size:16 final size:17
Alignment explanation
Indices: 1965937--1965968 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1965927 AAAATCTGAA
1965937 TTTATTTTTATTAATTC
1 TTTATTTTTATTAATTC
1965954 TTTA-TTTTATTAATT
1 TTTATTTTTATTAATT
1965969 ATATTTCTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTATTTTTATTAATTC
Done.