Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008243.1 Hibiscus syriacus cultivar Beakdansim tig00110893_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: 10265705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 49
Found at i:959449 original size:17 final size:17
Alignment explanation
Indices: 959391--959450 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
959381 CAGCATTTCC
*
959391 AGAAGGAGTTCACAATG
1 AGAAGAAGTTCACAATG
*
959408 AGAAGAA-CTCATCTGAA-G
1 AGAAGAAGTTCA-C--AATG
959426 AAGAAGAAGTTCACAATG
1 -AGAAGAAGTTCACAATG
959444 AGAAGAA
1 AGAAGAA
959451 CTTGTTCAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 12
0.69 0.06 0.24
Matches are distributed among these distances:
16 3 0.09
17 16 0.47
18 2 0.06
19 10 0.29
20 3 0.09
ACGTcount: A:0.48, C:0.12, G:0.25, T:0.15
Consensus pattern (17 bp):
AGAAGAAGTTCACAATG
Found at i:959708 original size:9 final size:9
Alignment explanation
Indices: 959694--959792 Score: 123
Period size: 9 Copynumber: 11.0 Consensus size: 9
959684 TTTTATTTAT
959694 TTATTATTA
1 TTATTATTA
959703 TTATTATTA
1 TTATTATTA
*
959712 TTATAATTA
1 TTATTATTA
959721 TTATTATTA
1 TTATTATTA
*
959730 TAATTATTA
1 TTATTATTA
959739 -TATATATTA
1 TTAT-TATTA
*
959748 TTATAATTA
1 TTATTATTA
959757 TTA-TATATA
1 TTATTAT-TA
959766 TTATTA-TA
1 TTATTATTA
959774 TATATTATTA
1 T-TATTATTA
959784 TTATTATTA
1 TTATTATTA
959793 AAAAATAATT
Statistics
Matches: 78, Mismatches: 6, Indels: 12
0.81 0.06 0.12
Matches are distributed among these distances:
8 7 0.09
9 63 0.81
10 8 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
TTATTATTA
Found at i:959711 original size:12 final size:12
Alignment explanation
Indices: 959694--959792 Score: 123
Period size: 12 Copynumber: 8.2 Consensus size: 12
959684 TTTTATTTAT
959694 TTATTATTATTA
1 TTATTATTATTA
*
959706 TTATTATTATAA
1 TTATTATTATTA
959718 TTATTATTATTA
1 TTATTATTATTA
*
959730 TAATTATTA-TA
1 TTATTATTATTA
*
959741 TATATTATTATAA
1 T-TATTATTATTA
959754 TTATTA-TATATA
1 TTATTATTAT-TA
959766 TTATTA-TATATA
1 TTATTATTAT-TA
959778 TTATTATTATTA
1 TTATTATTATTA
959790 TTA
1 TTA
959793 AAAAATAATT
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
11 6 0.08
12 66 0.86
13 5 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTATTATTATTA
Found at i:959722 original size:21 final size:21
Alignment explanation
Indices: 959697--959792 Score: 126
Period size: 21 Copynumber: 4.6 Consensus size: 21
959687 TATTTATTTA
* *
959697 TTATTATTATTATTATTATAA
1 TTATTATTATTATAATTATTA
959718 TTATTATTATTATAATTATTA
1 TTATTATTATTATAATTATTA
959739 -TATATATTATTATAATTATTA
1 TTAT-TATTATTATAATTATTA
959760 -TATATATTATTAT-ATATATTA
1 TTAT-TATTATTATAAT-TATTA
959781 TTATTATTATTA
1 TTATTATTATTA
959793 AAAAATAATT
Statistics
Matches: 70, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
20 5 0.07
21 62 0.89
22 3 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTATTATTATTATAATTATTA
Found at i:962695 original size:76 final size:76
Alignment explanation
Indices: 962569--962750 Score: 292
Period size: 76 Copynumber: 2.4 Consensus size: 76
962559 CTATTTCCCA
*
962569 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
* *
962634 AGCCTTAGGGT
66 AACCTTAGAGT
*
962645 CATCTATAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
*
962710 AACCTTCGAGT
66 AACCTTAGAGT
* * *
962721 CAGCTGTAAGCCCTACAGTGCATAATGTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTT
962751 TTTTAAACTT
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 97 1.00
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
AACCTTAGAGT
Found at i:962966 original size:113 final size:112
Alignment explanation
Indices: 962763--963189 Score: 446
Period size: 113 Copynumber: 3.7 Consensus size: 112
962753 TTAAACTTTT
* * *
962763 CCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAAAAGTTCATAATGAGAAGA
1 CCAGATAGAGTTCATAATGAGAAGAACTTATCTGAAG-AAGAAGAAGAAGTTCATAATGAGAAGA
* *
962828 ACTTGTTCAACCTTTTGCTCAAATTCATCACTCGGTGGATCAACAATG
65 ACTTGTTCAACCTTTCGCTCAAATTCATCACTCGATGGATCAACAATG
* *
962876 CCAGTTAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGA
1 CCAGATAGAGTTCATAATGAGAAGAACTTATCTGAAGAA-GAAGAAGAAGTTCATAATGAGAAGA
* ** * * ** *
962941 ATTTGTTCAACCTTTCGCTTTAATTCATCACTCGATGGATTAGCTTTT
65 ACTTGTTCAACCTTTCGCTCAAATTCATCACTCGATGGATCAACAATG
* * * *
962989 CCAAAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAG
1 CCAGATAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAA
* * ** * *
963054 CTTGTTCAACCTTT-G-T-ATGACTCTATCACAGAAAGAGATAGATCAACACCAACTTTT
66 CTTGTTCAACCTTTCGCTCA-AATTC-ATCAC-----TCGATGGATC-A-A-CAA---TG
* * *
963111 CCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAGGAAGTTCATAATGAGAAGAA
1 CCAGATAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAA
963176 CTTGTTCAACCTTT
66 CTTGTTCAACCTTT
963190 TGCATGACGC
Statistics
Matches: 266, Mismatches: 34, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
110 4 0.02
111 6 0.02
112 39 0.15
113 131 0.49
116 6 0.02
117 1 0.00
119 1 0.00
122 78 0.29
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.26
Consensus pattern (112 bp):
CCAGATAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAA
CTTGTTCAACCTTTCGCTCAAATTCATCACTCGATGGATCAACAATG
Found at i:963120 original size:122 final size:123
Alignment explanation
Indices: 962984--963313 Score: 504
Period size: 123 Copynumber: 2.7 Consensus size: 123
962974 GATGGATTAG
*
962984 CTTTTCCAAAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAAGAAGTTCATAATGAG
1 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAAGAAGTTCATAATGAG
* * *
963049 AAGAGCTTGTTCAACC-TTTGTATGACTCTATCACAGAAA-GAGATAGATCAACACCAA
66 AAGAACTTGTTCAACCTTTTGCATGACGCTATCACA-AAAGGAGATAGATCAACACCAA
*
963106 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAGGAAGTTCATAATGAG
1 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAAGAAGTTCATAATGAG
* *
963171 AAGAACTTGTTCAACCTTTTGCATGACGCTATCACAAAAGGAGATAGATCGACATCAA
66 AAGAACTTGTTCAACCTTTTGCATGACGCTATCACAAAAGGAGATAGATCAACACCAA
* * *
963229 CATTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAATG-AGAAGAAGTTCATAATGA
1 CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAA-GAAGAAGAAGTTCATAATGA
* * *
963293 GAAGAATTTATTCAACTTTTT
65 GAAGAACTTGTTCAACCTTTT
963314 TCTAAATCAC
Statistics
Matches: 191, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
122 81 0.42
123 109 0.57
124 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.26
Consensus pattern (123 bp):
CTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAAGAAGTTCATAATGAG
AAGAACTTGTTCAACCTTTTGCATGACGCTATCACAAAAGGAGATAGATCAACACCAA
Found at i:963534 original size:3 final size:3
Alignment explanation
Indices: 963528--963586 Score: 66
Period size: 3 Copynumber: 19.0 Consensus size: 3
963518 TTGATTTTTT
* *
963528 TTA TTA -TA TTTA TTTA TTA CTA TTA TTA TTA TTA TTA TTA TTAA ATA
1 TTA TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA
963575 TTA TTA TTA TTA
1 TTA TTA TTA TTA
963587 CATTGCAGGC
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 2 0.04
3 39 0.80
4 8 0.16
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:970411 original size:37 final size:37
Alignment explanation
Indices: 970335--970411 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
970325 TTTTTATATT
*
970335 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
970372 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
970409 TTT
1 TTT
970412 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:970593 original size:20 final size:20
Alignment explanation
Indices: 970557--970594 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
970547 ATCCTATTCC
**
970557 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
970577 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
970595 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:970945 original size:2 final size:2
Alignment explanation
Indices: 970938--970983 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
970928 AATTGTTCCA
970938 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
970980 AT AT
1 AT AT
970984 TGTAATACTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:971881 original size:21 final size:23
Alignment explanation
Indices: 971857--971904 Score: 55
Period size: 25 Copynumber: 2.1 Consensus size: 23
971847 ATGTGCAGTT
*
971857 AATATGCT-AATATAA-TTAGTG
1 AATAAGCTAAATATAAGTTAGTG
971878 AATAAGCTGAAAATATAAGTTAGTG
1 AATAAGCT--AAATATAAGTTAGTG
971903 AA
1 AA
971905 ATCTACCCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 7 0.32
24 7 0.32
25 8 0.36
ACGTcount: A:0.48, C:0.04, G:0.17, T:0.31
Consensus pattern (23 bp):
AATAAGCTAAATATAAGTTAGTG
Found at i:972867 original size:19 final size:19
Alignment explanation
Indices: 972826--972868 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
972816 TGCATTGAGT
* **
972826 TATGAATTTGAAAATAAGG
1 TATGAATATGAAAATAAAC
972845 TATGAATATGAAAATAAAC
1 TATGAATATGAAAATAAAC
972864 TATGA
1 TATGA
972869 GTCTGGAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.51, C:0.02, G:0.16, T:0.30
Consensus pattern (19 bp):
TATGAATATGAAAATAAAC
Found at i:973503 original size:18 final size:19
Alignment explanation
Indices: 973480--973527 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
973470 AATTAAAGTT
*
973480 TTATATTTTA-GATAAAAA
1 TTATATTTTATGAGAAAAA
973498 TTATATTTTATGAGAAAAA
1 TTATATTTTATGAGAAAAA
*
973517 TAAATATTTTA
1 T-TATATTTTA
973528 AAATTAGGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 10 0.38
19 8 0.31
20 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (19 bp):
TTATATTTTATGAGAAAAA
Found at i:974054 original size:18 final size:19
Alignment explanation
Indices: 974031--974066 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
974021 GATCCAAATC
974031 CTAATC-CCTAAATTATAA
1 CTAATCTCCTAAATTATAA
974049 CTAATCTCCTAAATTATA
1 CTAATCTCCTAAATTATA
974067 CCCTAAATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.42, C:0.22, G:0.00, T:0.36
Consensus pattern (19 bp):
CTAATCTCCTAAATTATAA
Found at i:974077 original size:19 final size:19
Alignment explanation
Indices: 974037--974082 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
974027 AATCCTAATC
*
974037 CCTAAATTATAACTAATCT
1 CCTAAATTATAACTAATAT
*
974056 CCTAAATTATACCCTAA-AT
1 CCTAAATTATA-ACTAATAT
974075 CCTAAATT
1 CCTAAATT
974083 CCAAATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.35
Consensus pattern (19 bp):
CCTAAATTATAACTAATAT
Found at i:975041 original size:6 final size:7
Alignment explanation
Indices: 975024--975048 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
975014 ATTATTTTAA
975024 AAAAATT
1 AAAAATT
975031 AAAAATT
1 AAAAATT
975038 AAAAATT
1 AAAAATT
975045 AAAA
1 AAAA
975049 CAAACTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAAATT
Found at i:979387 original size:19 final size:19
Alignment explanation
Indices: 979363--979412 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
979353 CCGGTTTTCA
*
979363 ACCGGTTCTGATCGGTTTG
1 ACCGGTTCTGACCGGTTTG
979382 ACCGGTTC-GAACCGGTTTG
1 ACCGGTTCTG-ACCGGTTTG
979401 ACCGG-TCTGACC
1 ACCGGTTCTGACC
979413 TGACCGACCC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.14, C:0.28, G:0.30, T:0.28
Consensus pattern (19 bp):
ACCGGTTCTGACCGGTTTG
Found at i:979404 original size:9 final size:9
Alignment explanation
Indices: 979363--979412 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
979353 CCGGTTTTCA
979363 ACCGGTTCTG
1 ACCGGTT-TG
*
979373 ATCGGTTTG
1 ACCGGTTTG
*
979382 ACCGGTTCG
1 ACCGGTTTG
979391 AACCGGTTTG
1 -ACCGGTTTG
*
979401 ACCGGTCTG
1 ACCGGTTTG
979410 ACC
1 ACC
979413 TGACCGACCC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 20 0.59
10 14 0.41
ACGTcount: A:0.14, C:0.28, G:0.30, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:986639 original size:10 final size:9
Alignment explanation
Indices: 986616--986656 Score: 55
Period size: 10 Copynumber: 4.3 Consensus size: 9
986606 GCTGCTGGAA
986616 ACCGGTTTG
1 ACCGGTTTG
986625 ACCGGTTTCG
1 ACCGGTTT-G
986635 ACCGGTTTG
1 ACCGGTTTG
*
986644 AACCGGTCTG
1 -ACCGGTTTG
986654 ACC
1 ACC
986657 CGACCGACCC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 12 0.41
10 17 0.59
ACGTcount: A:0.15, C:0.29, G:0.29, T:0.27
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:986656 original size:19 final size:19
Alignment explanation
Indices: 986616--986656 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
986606 GCTGCTGGAA
*
986616 ACCGGTTTGACCGGTTTCG
1 ACCGGTTTGACCGGTCTCG
986635 ACCGGTTTGAACCGGTCT-G
1 ACCGGTTTG-ACCGGTCTCG
986654 ACC
1 ACC
986657 CGACCGACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.15, C:0.29, G:0.29, T:0.27
Consensus pattern (19 bp):
ACCGGTTTGACCGGTCTCG
Found at i:990400 original size:16 final size:17
Alignment explanation
Indices: 990381--990413 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
990371 AATTTAAATA
990381 TATTTA-TAAAAATATT
1 TATTTATTAAAAATATT
990397 TATTTATTTAAAAATAT
1 TATTTA-TTAAAAATAT
990414 CAGAAAAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTTATTAAAAATATT
Found at i:990734 original size:37 final size:37
Alignment explanation
Indices: 990664--990734 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
990654 ATTTAAACAT
* *
990664 ATAAAATTAAAATATAAATAAACAATGAGTAAAATAG
1 ATAAAATTAAAATATAAATAAAAAATGAATAAAATAG
990701 ATAAAATTAAAAT-TAAATATAAAAA-GTAATAAAA
1 ATAAAATTAAAATATAAATA-AAAAATG-AATAAAA
990735 CTTATAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 7 0.23
37 23 0.77
ACGTcount: A:0.68, C:0.01, G:0.06, T:0.25
Consensus pattern (37 bp):
ATAAAATTAAAATATAAATAAAAAATGAATAAAATAG
Found at i:992019 original size:3 final size:3
Alignment explanation
Indices: 992000--992046 Score: 67
Period size: 3 Copynumber: 15.0 Consensus size: 3
991990 TTGTAATATT
*
992000 TAA TAAA TAA TATA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
992047 ATTTAAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 34 0.85
4 6 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:992230 original size:45 final size:45
Alignment explanation
Indices: 992180--992282 Score: 188
Period size: 45 Copynumber: 2.3 Consensus size: 45
992170 GATGAAAATG
* *
992180 TTTGAAAACATCATGCACTGCAGGGCTTACGGATGACCCGAAGGC
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGC
992225 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGC
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGC
992270 TTTGAAAACATCA
1 TTTGAAAACATCA
992283 AAAAGCTCCC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.21
Consensus pattern (45 bp):
TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGC
Found at i:992340 original size:76 final size:74
Alignment explanation
Indices: 992216--992358 Score: 250
Period size: 76 Copynumber: 1.9 Consensus size: 74
992206 TTACGGATGA
992216 CCCGAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACAT
1 CCCGAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACAT
992281 CAAAAAGCT
66 CAAAAAGCT
* *
992290 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACGGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGC--TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
992355 ATCA
64 ATCA
992359 TGCACTGAAG
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
74 9 0.14
76 56 0.86
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (74 bp):
CCCGAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACAT
CAAAAAGCT
Found at i:992362 original size:45 final size:45
Alignment explanation
Indices: 992290--992403 Score: 183
Period size: 45 Copynumber: 2.5 Consensus size: 45
992280 TCAAAAAGCT
* *
992290 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACGGATGA
1 CCCGAAGGC--TTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
992337 CCCGAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
992382 CTCGAAGGCTTTGAAAACATCA
1 CCCGAAGGCTTTGAAAACATCA
992404 AAAAGCTCCC
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
45 55 0.86
47 9 0.14
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.22
Consensus pattern (45 bp):
CCCGAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
Found at i:992399 original size:121 final size:122
Alignment explanation
Indices: 992180--992480 Score: 559
Period size: 121 Copynumber: 2.5 Consensus size: 122
992170 GATGAAAATG
*
992180 TTTGAAAACATCATGCACTGCAGGGCTTACGGATGACCCGAAGGCTTTGAAAACATCATGCACTG
1 TTTGAAAACATCATGCACTGAAGGGCTTACGGATGACCCGAAGGCTTTGAAAACATCATGCACTG
992245 AAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC-TT
66 AAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCGTT
*
992301 TTTGGAAACATCATGCACTGAAGGGCTTACGGATGACCCGAAGGCTTTGAAAACATCATGCACTG
1 TTTGAAAACATCATGCACTGAAGGGCTTACGGATGACCCGAAGGCTTTGAAAACATCATGCACTG
*
992366 AAGGGCTTACAGATGACTCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCGTT
66 AAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCGTT
*
992423 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCA
1 TTTGAAAACATCATGCACTGAAGGGCTTACGGATGACCCGAAGGCTTTGAAAACATCA
992481 AAAAGCTCCC
Statistics
Matches: 174, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
121 116 0.67
122 58 0.33
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.21
Consensus pattern (122 bp):
TTTGAAAACATCATGCACTGAAGGGCTTACGGATGACCCGAAGGCTTTGAAAACATCATGCACTG
AAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCGTT
Found at i:992625 original size:76 final size:76
Alignment explanation
Indices: 992337--992633 Score: 490
Period size: 77 Copynumber: 3.9 Consensus size: 76
992327 TTACGGATGA
*
992337 CCCGAAGGC--TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACTCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
992400 ATCAAAAAGCT
66 ATCAAAAAGCT
992411 CCCGAAGGCGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
1 CCCGAAGGC-TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
992476 CATCAAAAAGCT
65 CATCAAAAAGCT
*
992488 CCCGAAGGCTTTTTGAAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
1 CCCGAAGGCTTTTTG-AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
*
992553 TATCAAAAAGCT
65 CATCAAAAAGCT
** * * *
992565 CTTGAAGGCTTTTTGAAAACATCCTGCACTGCAGGGCTTACGGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
992630 ATCA
66 ATCA
992634 TGCACTGAAG
Statistics
Matches: 209, Mismatches: 10, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
74 9 0.04
76 55 0.26
77 145 0.69
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
ATCAAAAAGCT
Found at i:992638 original size:45 final size:45
Alignment explanation
Indices: 992576--992678 Score: 179
Period size: 45 Copynumber: 2.3 Consensus size: 45
992566 TTGAAGGCTT
* * *
992576 TTTGAAAACATCCTGCACTGCAGGGCTTACGGATGACCCGAAGGC
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGC
992621 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGC
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGC
992666 TTTGAAAACATCA
1 TTTGAAAACATCA
992679 AAAAGCTCCC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.21
Consensus pattern (45 bp):
TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGC
Found at i:992641 original size:121 final size:121
Alignment explanation
Indices: 992488--992754 Score: 426
Period size: 121 Copynumber: 2.2 Consensus size: 121
992478 TCAAAAAGCT
*
992488 CCCGAAGGCTTTTTGAAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
1 CCCGAAGGC--TTTG-AAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
* ** * * *
992553 TATCAAAAAGCTCTTGAAGGCTTTTTGAAAACATCCTGCACTGCAGGGCTTACGGATGA
63 CATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGCAGGACTTACAGATGA
992612 CCCGAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACAT
1 CCCGAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACAT
*
992677 CAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGACTTACAGATGA
66 CAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGCAGGACTTACAGATGA
*
992733 CCCTAAGGCTTTGAAAACATCA
1 CCCGAAGGCTTTGAAAACATCA
992755 AAAAGCTCCC
Statistics
Matches: 134, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
121 121 0.90
122 4 0.03
124 9 0.07
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (121 bp):
CCCGAAGGCTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACAT
CAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGCAGGACTTACAGATGA
Found at i:992701 original size:76 final size:76
Alignment explanation
Indices: 992612--992807 Score: 342
Period size: 76 Copynumber: 2.6 Consensus size: 76
992602 TTACGGATGA
* *
992612 CCCGAAGGC--TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
992675 ATCAAAAAGCT
66 ATCAAAAAGCT
*
992686 CCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
992751 ATCAAAAAGCT
66 ATCAAAAAGCT
*
992762 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
1 CCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGACTTACAGATG
992808 TGGGAAATAG
Statistics
Matches: 116, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
74 9 0.08
76 107 0.92
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (76 bp):
CCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
ATCAAAAAGCT
Found at i:993505 original size:22 final size:21
Alignment explanation
Indices: 993477--993528 Score: 72
Period size: 19 Copynumber: 2.5 Consensus size: 21
993467 CCCATAAGCT
993477 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAA-AGAATCTA
*
993499 TCATCTTT--AAAATAATCTA
1 TCATCTTTGAAAAAGAATCTA
993518 TCATCTTTGAA
1 TCATCTTTGAA
993529 GAGTGTAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 15 0.56
20 3 0.11
21 1 0.04
22 8 0.30
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (21 bp):
TCATCTTTGAAAAAGAATCTA
Found at i:994994 original size:76 final size:75
Alignment explanation
Indices: 994869--995045 Score: 205
Period size: 76 Copynumber: 2.3 Consensus size: 75
994859 AGGATGTTGT
* * * * *
994869 GGGCCTTCAGCATGCCCCAATATTTGCTGATATGAGCGTTCAAAATACATCAACATTCTTCATTC
1 GGGCTTTCAGCATGCCCCAATATTTGCTGATATAAACATTCAAAATACATCAACATTCCTCATTC
994934 TGATTGA-AA
66 TGATTGACAA
* ** *
994943 GGGGCTTTCAGCATGCCCTAGCAT-TTTGCTGATATAAACATTCAGGATACATCAACATTCCTGA
1 -GGGCTTTCAGCATGCCCCA--ATATTTGCTGATATAAACATTCAAAATACATCAACATTCCTCA
*
995007 TTTTGATTGACAA
63 TTCTGATTGACAA
* *
995020 GGGTTTTCAGCATGCCCCAACATTTG
1 GGGCTTTCAGCATGCCCCAATATTTG
995046 TTTCTTGTTA
Statistics
Matches: 85, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
74 1 0.01
75 21 0.25
76 59 0.69
77 4 0.05
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (75 bp):
GGGCTTTCAGCATGCCCCAATATTTGCTGATATAAACATTCAAAATACATCAACATTCCTCATTC
TGATTGACAA
Found at i:996222 original size:114 final size:114
Alignment explanation
Indices: 996022--996235 Score: 338
Period size: 114 Copynumber: 1.9 Consensus size: 114
996012 GATCATGCAG
* * * *
996022 TTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAAATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGAGGTTCATACCAAACCAAATCAGATAACTCAAAGA
*
996087 ATACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTATTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTATTATGAGCAAA
* * * *
996136 TTCATCTTTCAAATCTAATGATTGGTTTTGAGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGAGGTTCATACCAAACCAAATCAGATAACTCAAAGA
*
996201 ACACTTCCAGAAGATGTTATTGGGTCTCCTTATTT
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTT
996236 TTACTACGAG
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 90 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGAGGTTCATACCAAACCAAATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTATTATGAGCAAA
Found at i:1001379 original size:269 final size:266
Alignment explanation
Indices: 1000886--1001422 Score: 1006
Period size: 269 Copynumber: 2.0 Consensus size: 266
1000876 CAACCTTGTT
*
1000886 TTGGATTGAACCTGAGTTTTAGACGTCGGGAGCAGACCAAACTTTGATGATTTTGATTACCTGAT
1 TTGGATTGAACCTGAGTTTTAGACGTCGGGAGCAGACCAAACTTTGATGATTTTGATTACATGAT
1000951 TTTTCTCATCTCTGGGAGCTTTTACGTGGTCAACATTTCTTTGGTATCTCCAGACGATTTGGAAT
66 TTTTCTCATCTCTGGGAGCTTTTACGTGGTCAACATTTCTTTGGTATCTCCAGACGATTTGGAAT
1001016 ACAAATGATGATTGTCTGCAACTTCTCAAATTGGTTAGGATCAAAGGCCCTTGCATATATGAAAT
131 ACAAATGATGATTGTCTGCAACTTCTCAAATTGGTTAGGATCAAAGGCCCTTGCATATATGAAAT
1001081 TGCAGGATTATCTTCATTAAGCTTTCTCTCTTTCTGTGCAGGAATCTC-T-TCTTTTGGCCAAAA
196 TGCAGGATTATCTTCATTAAGCTTTCTCTCTTTCTGTGCAGGAATCTCTTCTCTTTTGGCCAAAA
1001144 CAGATA
261 CAGATA
1001150 TTGGATTGAACCTGAGTTTTAGACGTCGGGAGCAGACCAAACTTTGATGATTTCTGATTACATGA
1 TTGGATTGAACCTGAGTTTTAGACGTCGGGAGCAGACCAAACTTTGATGATTT-TGATTACATGA
1001215 TTTCTTCTCATCTCTGGGAGCTTTTACAGTGGTCAACATTTCTTTGGTATCTCCAGACGATTTGT
65 TTT-TTCTCATCTCTGGGAGCTTTTAC-GTGGTCAACATTTCTTTGGTATCTCCAGACGATTTG-
1001280 GAATACAAATGATGATTGTCTGCAACTTCTCAAATTGGTTAGGATCAAAAGGCCCTTGCATATAT
127 GAATACAAATGATGATTGTCTGCAACTTCTCAAATTGGTTAGGATC-AAAGGCCCTTGCATATAT
1001345 GAAATTGCAGGATTATCTTCATTAAGCTTTCTCTCTTTCTGTGCAGGAATCTCTTCTCTTTTGGC
191 GAAATTGCAGGATTATCTTCATTAAGCTTTCTCTCTTTCTGTGCAGGAATCTCTTCTCTTTTGGC
1001410 CAAAACAGATA
256 CAAAACAGATA
1001421 TT
1 TT
1001423 CTATCCATCA
Statistics
Matches: 265, Mismatches: 1, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
264 53 0.20
265 13 0.05
266 23 0.09
267 36 0.14
268 46 0.17
269 71 0.27
270 1 0.00
271 22 0.08
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (266 bp):
TTGGATTGAACCTGAGTTTTAGACGTCGGGAGCAGACCAAACTTTGATGATTTTGATTACATGAT
TTTTCTCATCTCTGGGAGCTTTTACGTGGTCAACATTTCTTTGGTATCTCCAGACGATTTGGAAT
ACAAATGATGATTGTCTGCAACTTCTCAAATTGGTTAGGATCAAAGGCCCTTGCATATATGAAAT
TGCAGGATTATCTTCATTAAGCTTTCTCTCTTTCTGTGCAGGAATCTCTTCTCTTTTGGCCAAAA
CAGATA
Found at i:1003140 original size:37 final size:37
Alignment explanation
Indices: 1003070--1003140 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
1003060 ATTTAAACAT
* *
1003070 ATAAAATTAAAATATAAATAAACAATGAGTAAAATAG
1 ATAAAATTAAAATATAAATAAAAAATGAATAAAATAG
1003107 ATAAAATTAAAAT-TAAATATAAAAA-GTAATAAAA
1 ATAAAATTAAAATATAAATA-AAAAATG-AATAAAA
1003141 CTTATAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 7 0.23
37 23 0.77
ACGTcount: A:0.68, C:0.01, G:0.06, T:0.25
Consensus pattern (37 bp):
ATAAAATTAAAATATAAATAAAAAATGAATAAAATAG
Found at i:1004422 original size:3 final size:3
Alignment explanation
Indices: 1004403--1004455 Score: 79
Period size: 3 Copynumber: 17.0 Consensus size: 3
1004393 TTGTAATATT
*
1004403 TAA TAAA TAA TATA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1004450 TAA TAA
1 TAA TAA
1004456 ATTTAAATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 40 0.87
4 6 0.13
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1009614 original size:12 final size:10
Alignment explanation
Indices: 1009573--1009613 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
1009563 TTTATCACAC
1009573 CAAATTCTCT
1 CAAATTCTCT
1009583 CAAATTCTCT
1 CAAATTCTCT
1009593 -AAATTTCTCT
1 CAAA-TTCTCT
*
1009603 CAAATACTCT
1 CAAATTCTCT
1009613 C
1 C
1009614 TTTTTAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:1011487 original size:18 final size:18
Alignment explanation
Indices: 1011464--1011499 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1011454 CCAGCAGCCA
1011464 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
1011482 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
1011500 GCGCCATCGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (18 bp):
CCGCAGCCATATATGATG
Found at i:1011850 original size:3 final size:3
Alignment explanation
Indices: 1011842--1011876 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
1011832 ACCTACACAA
*
1011842 GAC GAC GAC GAC GAC TAC GAC GAC GAC GAC GAC GA
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GA
1011877 TGGTGATGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.34, C:0.31, G:0.31, T:0.03
Consensus pattern (3 bp):
GAC
Found at i:1015708 original size:49 final size:51
Alignment explanation
Indices: 1015598--1015720 Score: 155
Period size: 49 Copynumber: 2.5 Consensus size: 51
1015588 TTATACAAAA
* *
1015598 CGCGGTACCTGC-CCAACGCTATATAAAATTATGTCAGGAGTAAAGGTATAT
1 CGCGGTACCTGCACC-GCGCTATATAAAATTATGTCAGGAGTAAAGGTATAG
* * *
1015649 CGTGTTACCTGCACCGCGCTATATAAAATTAT-T-AGTAGTAAAGGTATAG
1 CGCGGTACCTGCACCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATAG
1015698 CGCGGTACCTG-ATCCGCGCTATA
1 CGCGGTACCTGCA-CCGCGCTATA
1015721 CCCCTACGTG
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
48 1 0.02
49 33 0.52
50 1 0.02
51 26 0.41
52 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (51 bp):
CGCGGTACCTGCACCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATAG
Found at i:1016279 original size:45 final size:45
Alignment explanation
Indices: 1016215--1016305 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
1016205 CAATAGATTA
1016215 ACATTCAACTTATATAATCGTCATTTTTTTAACAAAAAAATGAAG
1 ACATTCAACTTATATAATCGTCATTTTTTTAACAAAAAAATGAAG
1016260 ACATTCAACTTATATAATCGTCATTTTTTTAACAAAAAAATGAAG
1 ACATTCAACTTATATAATCGTCATTTTTTTAACAAAAAAATGAAG
1016305 A
1 A
1016306 ACTTGGAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.45, C:0.13, G:0.07, T:0.35
Consensus pattern (45 bp):
ACATTCAACTTATATAATCGTCATTTTTTTAACAAAAAAATGAAG
Found at i:1025325 original size:20 final size:21
Alignment explanation
Indices: 1025297--1025338 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1025287 CTAACCTCTT
*
1025297 ATCTATAAATCTAAACTTTAA
1 ATCTATAAATCTAAACCTTAA
*
1025318 ATCT-TAAATTTAAACCTTAA
1 ATCTATAAATCTAAACCTTAA
1025338 A
1 A
1025339 AATTCATACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (21 bp):
ATCTATAAATCTAAACCTTAA
Found at i:1027263 original size:36 final size:36
Alignment explanation
Indices: 1027216--1027284 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
1027206 GAACACTTTG
* *
1027216 AAAAATAAATAAAGGAACACAAACATAATTTATATC
1 AAAAATAAATAAAAGAACACAAACATAACTTATATC
*
1027252 AAAAATAAATAAAAGAACACAAACGTAACTTAT
1 AAAAATAAATAAAAGAACACAAACATAACTTAT
1027285 TTCGTTCTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.62, C:0.12, G:0.06, T:0.20
Consensus pattern (36 bp):
AAAAATAAATAAAAGAACACAAACATAACTTATATC
Found at i:1028129 original size:69 final size:69
Alignment explanation
Indices: 1028018--1028162 Score: 272
Period size: 69 Copynumber: 2.1 Consensus size: 69
1028008 TCAAGTTGTC
*
1028018 AATTAACCTTAATCCAACAAAGAAACAACTTGTTGCCAATGGATTCAAAGCATTTGCAGTGAAAA
1 AATTAACCTTAATCCAACAAAGAAACAACTTGTTGCCAATGGATTCAAAGCATCTGCAGTGAAAA
1028083 TGGA
66 TGGA
*
1028087 AATTAAGCTTAATCCAACAAAGAAACAACTTGTTGCCAATGGATTCAAAGCATCTGCAGTGAAAA
1 AATTAACCTTAATCCAACAAAGAAACAACTTGTTGCCAATGGATTCAAAGCATCTGCAGTGAAAA
1028152 TGGA
66 TGGA
1028156 AATTAAC
1 AATTAAC
1028163 TGTGTGGTTG
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 73 1.00
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.24
Consensus pattern (69 bp):
AATTAACCTTAATCCAACAAAGAAACAACTTGTTGCCAATGGATTCAAAGCATCTGCAGTGAAAA
TGGA
Found at i:1030455 original size:15 final size:15
Alignment explanation
Indices: 1030430--1030501 Score: 83
Period size: 15 Copynumber: 4.9 Consensus size: 15
1030420 TTAGTTTTCA
1030430 GAAAATGAATTACTG
1 GAAAATGAATTACTG
**
1030445 GAATTTGAATTACTG
1 GAAAATGAATTACTG
*
1030460 AAAAATGAATTACTG
1 GAAAATGAATTACTG
* **
1030475 TAATTTGAATT-CTG
1 GAAAATGAATTACTG
1030489 GAAAATGAATTAC
1 GAAAATGAATTAC
1030502 ATTTCTGTAA
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
14 11 0.24
15 34 0.76
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (15 bp):
GAAAATGAATTACTG
Found at i:1030463 original size:29 final size:29
Alignment explanation
Indices: 1030430--1030501 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 29
1030420 TTAGTTTTCA
1030430 GAAAATGAATTACTGGAATTTGAATTACTG
1 GAAAATGAATTACTGGAATTTGAATT-CTG
* *
1030460 AAAAATGAATTACTGTAATTTGAATTCTG
1 GAAAATGAATTACTGGAATTTGAATTCTG
1030489 GAAAATGAATTAC
1 GAAAATGAATTAC
1030502 ATTTCTGTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 15 0.38
30 24 0.62
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (29 bp):
GAAAATGAATTACTGGAATTTGAATTCTG
Found at i:1030507 original size:20 final size:20
Alignment explanation
Indices: 1030484--1030553 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
1030474 GTAATTTGAA
1030484 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
1030504 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
1030524 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
1030544 TTCTGGAAAA
1 TTCTGGAAAA
1030554 CATCTGGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:1030767 original size:27 final size:27
Alignment explanation
Indices: 1030714--1030813 Score: 80
Period size: 27 Copynumber: 3.6 Consensus size: 27
1030704 CTTTACTAAA
* **
1030714 ATATTATTGAAATATATAATAGTATTAT
1 ATATTATT-AAATATATAAAAAAATTAT
1030742 -TCATTATTAAATATATAAAAAAATTAT
1 AT-ATTATTAAATATATAAAAAAATTAT
*
1030769 ATATTATTAAA-ATA-AAAATATAATATCTT
1 ATATTATTAAATATATAAAA-A-AAT-T-AT
1030798 ATATTATTATAATATA
1 ATATTATTA-AATATA
1030814 ATGATTATTT
Statistics
Matches: 60, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
25 4 0.07
26 4 0.07
27 29 0.48
28 8 0.13
29 10 0.17
30 2 0.03
31 3 0.05
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (27 bp):
ATATTATTAAATATATAAAAAAATTAT
Found at i:1030842 original size:14 final size:14
Alignment explanation
Indices: 1030825--1030873 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
1030815 TGATTATTTT
1030825 ATATAATATTAAAA
1 ATATAATATTAAAA
*
1030839 ATATAATATTATATA
1 ATATAATATTA-AAA
* *
1030854 TTAAAATATTAATAA
1 ATATAATATTAA-AA
1030869 ATATA
1 ATATA
1030874 TTTTAAATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
14 12 0.44
15 15 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATAATATTAAAA
Found at i:1030856 original size:21 final size:20
Alignment explanation
Indices: 1030830--1030875 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1030820 ATTTTATATA
*
1030830 ATATTAAAA-ATATAATATTAT
1 ATATTAAAATAT-TAATA-AAT
1030851 ATATTAAAATATTAATAAAT
1 ATATTAAAATATTAATAAAT
1030871 ATATT
1 ATATT
1030876 TTAAATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 7 0.30
21 14 0.61
22 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATTAAAATATTAATAAAT
Found at i:1030861 original size:29 final size:31
Alignment explanation
Indices: 1030798--1030873 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 31
1030788 ATAATATCTT
*
1030798 ATATTATTATAATATAATGATTATTTTATATA
1 ATATTAATA-AATATAATGATTATTTTATATA
1030830 ATATTAA-AAATATAAT-ATTATATATTA-A-A
1 ATATTAATAAATATAATGATTAT-T-TTATATA
1030859 ATATTAATAAATATA
1 ATATTAATAAATATA
1030874 TTTTAAATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
29 13 0.32
30 17 0.43
31 4 0.10
32 6 0.15
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (31 bp):
ATATTAATAAATATAATGATTATTTTATATA
Found at i:1030872 original size:20 final size:21
Alignment explanation
Indices: 1030830--1030875 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
1030820 ATTTTATATA
*
1030830 ATATTAAAAATATAATATTAT
1 ATATTAAAAATATAATATAAT
1030851 ATATT-AAAATATTAATA-AAT
1 ATATTAAAAATA-TAATATAAT
1030871 ATATT
1 ATATT
1030876 TTAAATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATATTAAAAATATAATATAAT
Found at i:1030876 original size:53 final size:50
Alignment explanation
Indices: 1030781--1030899 Score: 125
Period size: 53 Copynumber: 2.3 Consensus size: 50
1030771 ATTATTAAAA
* * *
1030781 TAAAAATATAATATCTTATATTATTATAATATAATGATTATTTTATATAATAT
1 TAAAAATATAATA--TTATATTATTAAAATATAATAATTATTTTAAAT-ATAT
*
1030834 TAAAAATATAATATTATA-TATTAAAATATTAATAAATATATTTTAAATATTT
1 TAAAAATATAATATTATATTATTAAAATA-TAAT-AAT-TATTTTAAATATAT
*
1030886 TAATAAT-TAATATT
1 TAAAAATATAATATT
1030900 TTGATGAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
50 9 0.16
51 16 0.28
52 11 0.19
53 22 0.38
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (50 bp):
TAAAAATATAATATTATATTATTAAAATATAATAATTATTTTAAATATAT
Found at i:1030890 original size:29 final size:30
Alignment explanation
Indices: 1030826--1030897 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
1030816 GATTATTTTA
*
1030826 TATAATATTAA-AAATATAATATTATATAT
1 TATAATATTAATAAATATAATATTAAATAT
* *
1030855 TAAAATATTAATAAATAT-ATTTTAAATAT
1 TATAATATTAATAAATATAATATTAAATAT
*
1030884 TTTAATAATTAATA
1 TATAAT-ATTAATA
1030898 TTTTGATGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 23 0.64
30 13 0.36
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
TATAATATTAATAAATATAATATTAAATAT
Found at i:1031132 original size:42 final size:42
Alignment explanation
Indices: 1031073--1031188 Score: 205
Period size: 42 Copynumber: 2.8 Consensus size: 42
1031063 ATGAATTACA
* *
1031073 TTCCGGAAAATGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1031115 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
1031157 TTCCGAAAAACGAATTACGTGAAACAAACACG
1 TTCCGGAAAACGAATTACGTGAAACAAACACG
1031189 AAAATTTGGG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.45, C:0.19, G:0.19, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:1033849 original size:30 final size:31
Alignment explanation
Indices: 1033815--1033931 Score: 109
Period size: 29 Copynumber: 3.8 Consensus size: 31
1033805 GAAACGTAAA
*
1033815 AATTAAATAA-ATATAATATATAAATATAGC
1 AATTAAATAATATATAATATATAAATATAGT
*
1033845 AATT-AATAATAT-TAAT-TATTAAATATAAT
1 AATTAAATAATATATAATATA-TAAATATAGT
* *
1033874 AAATAATTAAAATATAATAATATATAAATATAGT
1 AATTAA--ATAATAT-ATAATATATAAATATAGT
* *
1033908 AATTAAA-AATAGATAATTTATAAA
1 AATTAAATAATATATAATATATAAA
1033932 AAAAATTATA
Statistics
Matches: 71, Mismatches: 8, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
28 2 0.03
29 20 0.28
30 18 0.25
31 4 0.06
32 7 0.10
34 18 0.25
35 2 0.03
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.37
Consensus pattern (31 bp):
AATTAAATAATATATAATATATAAATATAGT
Found at i:1033861 original size:13 final size:14
Alignment explanation
Indices: 1033815--1033900 Score: 56
Period size: 13 Copynumber: 6.1 Consensus size: 14
1033805 GAAACGTAAA
1033815 AATTAAATAA-ATAT
1 AATT-AATAATATAT
*
1033829 AA-TATATAAATATAGC
1 AATTA-AT-AATATA-T
1033845 AATTAATAATAT-T
1 AATTAATAATATAT
*
1033858 AATTATTAA-ATAT
1 AATTAATAATATAT
* *
1033871 AATAAATAAT-TAA
1 AATTAATAATATAT
1033884 AATATAATAATATAT
1 AAT-TAATAATATAT
1033899 AA
1 AA
1033901 ATATAGTAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 17
0.69 0.10 0.21
Matches are distributed among these distances:
12 3 0.05
13 24 0.44
14 10 0.18
15 12 0.22
16 4 0.07
17 2 0.04
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (14 bp):
AATTAATAATATAT
Found at i:1036425 original size:2 final size:2
Alignment explanation
Indices: 1036413--1036444 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1036403 ATATAATAGT
*
1036413 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1036445 ATAACATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1036968 original size:35 final size:37
Alignment explanation
Indices: 1036906--1036997 Score: 109
Period size: 35 Copynumber: 2.6 Consensus size: 37
1036896 GGATCATATC
* * *
1036906 TTTAG-GAGTTTAAAACATAGCAAAATTCTATCCTAT
1 TTTAGAGAGTTTGAATCCTAGCAAAATTCTATCCTAT
* *
1036942 TTTAG-GAG-TTGAATCCTAGCAGAATTCTATCTTAT
1 TTTAGAGAGTTTGAATCCTAGCAAAATTCTATCCTAT
*
1036977 TTTTGAGAGTTTGAATCCTAG
1 TTTAGAGAGTTTGAATCCTAG
1036998 TAGGACGAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
35 26 0.54
36 11 0.23
37 11 0.23
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (37 bp):
TTTAGAGAGTTTGAATCCTAGCAAAATTCTATCCTAT
Found at i:1037764 original size:106 final size:104
Alignment explanation
Indices: 1037458--1038315 Score: 806
Period size: 98 Copynumber: 8.3 Consensus size: 104
1037448 AATATTGTTC
* * * * *
1037458 CGAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACCGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAAC-TGAAAATGTTTGTTGACA
** * *
1037523 GTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCT
64 ACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
* * * *
1037564 CGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AAC-G-AAAT-CTTGTTGACAAT
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGAAAATGTTTGTTGACAAC
* * *
1037625 CAGCCGTCCCTTTGTTGTGAAGTTGAACTTGTGTTATCT
66 CAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
* *
1037664 CGAGTCCAATATCCTTCGCTGCGAAGTTGAAATTGGCTCTGAAATTTGAAAAATGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA-CTG-AAAATGTTTGTTGACA
*
1037729 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
64 ACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
* * * ** *
1037770 CGAGTGGCACGATATCC-TCTG-TCGTGGAGTTGAAA-TCGCGGATGAAACTGAAAATTTGTTCG
1 CGAGT--C-CAATATCCTTC-GCT-GTGAAGTTGAAATTGGC-TCTGAAACTGAAAA--TGTTTG
* *
1037832 TTGACAACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
58 TTGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
* * * * * * * *
1037879 CGGGTAGCACGATATCCTCCG-TCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAATTGTTTGTT
1 CGAGT--C-CAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAACT--GAAAATGTTTGTT
1037943 GACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
60 GACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
* * * * *
1037988 CGAATCCAATATCCTTCGCTGTGAAGTTGAGATTGGCTC-----C-G-AAATTTCTTGTCGACAG
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGAAAATGT-TTGTTGACAA
* * * * *
1038046 TCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGCTGTCT
65 CCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
* * * * * **
1038086 TGGGTCCAATATCCTTCGCTGTGAAGTTGAGATTGGCTC-----C-GAAATTGTTTGTCGACAGT
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGAAAATGTTTGTTGACAAC
* * *
1038145 CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
66 CAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
* * * * * *
1038184 TGGGTCCAATATCCTTCGCTGTGAAGTTGAAATTAGCCCTAAAACTGGGAAAT-TATTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACT-GAAAATGT-TTGTTGACA
* *
1038248 ACCAGCCGTCCCTTCGTTGTAAAGTTGAACTTGTGTTGTCT
64 ACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
1038289 CGAGTCCAATATCCTTCGCTGTGAAGT
1 CGAGTCCAATATCCTTCGCTGTGAAGT
1038316 CAAAATTGAC
Statistics
Matches: 642, Mismatches: 81, Indels: 59
0.82 0.10 0.08
Matches are distributed among these distances:
97 4 0.01
98 167 0.26
99 4 0.01
100 82 0.13
101 5 0.01
102 1 0.00
103 2 0.00
104 3 0.00
105 76 0.12
106 114 0.18
107 6 0.01
108 9 0.01
109 162 0.25
110 3 0.00
111 4 0.01
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (104 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGAAAATGTTTGTTGACAAC
CAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
Found at i:1037848 original size:109 final size:107
Alignment explanation
Indices: 1037507--1037990 Score: 514
Period size: 109 Copynumber: 4.6 Consensus size: 107
1037497 TGGAACCGGG
** * * *
1037507 AAATTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGT-CT
1 AAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGC-
* * * *
1037571 A--ATATCCT-TCG-CTGTGAAGTTGAAATTGACTCTG-AA-CG-
65 ACGATATCCTCT-GTC-GTGGAGTTGAAATCGGCTCTGAAATTGA
* * * *
1037609 AAA-T-CTTGTTGACAATCAGCCGTCCCTTTGTTGTGAAGTTGAACTTGTGTTATCTCGAGT-C-
1 AAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCA
* *
1037670 CAATAT-C-CT-TCGCTGCGAAGTTGAAATTGGCTCTGAAATTTGA
66 CGATATCCTCTGTCG-TG-G-AGTTGAAATCGGCTCTGAAA-TTGA
*
1037713 AAAATGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGC
1 AAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GC
** *
1037778 ACGATATCCTCTGTCGTGGAGTTGAAATC-GCGGATGAAACTGA
65 ACGATATCCTCTGTCGTGGAGTTGAAATCGGC-TCTGAAATTGA
* * *
1037821 AAATTTGTTCGTTGACAACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGTAG
1 AAA-TTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-G
* * *
1037886 CACGATATCCTCCGTCGTGGAGTTGAAATCGGCTCTGGAATTGGG
64 CACGATATCCTCTGTCGTGGAGTTGAAATCGGCTCTGAAATT-GA
*
1037931 AAATTGTTTGTTGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGA
1 AAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGA
1037991 ATCCAATATC
Statistics
Matches: 325, Mismatches: 34, Indels: 39
0.82 0.09 0.10
Matches are distributed among these distances:
97 1 0.00
98 3 0.01
99 2 0.01
100 70 0.22
101 3 0.01
102 3 0.01
103 1 0.00
104 3 0.01
105 1 0.00
106 52 0.16
108 9 0.03
109 162 0.50
110 8 0.02
111 4 0.01
112 3 0.01
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (107 bp):
AAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCA
CGATATCCTCTGTCGTGGAGTTGAAATCGGCTCTGAAATTGA
Found at i:1037950 original size:218 final size:205
Alignment explanation
Indices: 1037458--1038303 Score: 720
Period size: 206 Copynumber: 4.1 Consensus size: 205
1037448 AATATTGTTC
* * **
1037458 CGAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACCGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTCCGC-GTGGAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACA
** * *
1037523 GTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCTAATATCCTTCGCTGTGA
65 ACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTTCGCTGTGA
* ** * * *
1037588 AGTTGAAATTGACTCTGAACGAAATCTTGTTGACAATCAGCCGTCCCTTTGTTGTGAAGTTGAAC
130 AGTTGAAATCGACGATGAACGAAATCTTGTTGACAACCAACCGTCCCTTCGTTGTGAAGTTGAAC
1037653 TTGTGTTATCT
195 TTGTGTTATCT
* * * * *
1037664 CGAGTCCAATATCCTTCGC-TGCGAAGTTGAAATTGGCTCTGAAATTTGAAAAATGTTTGTTGAC
1 CGAGTCCAATATCCTCCGCGTG-G-AGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGAC
*
1037728 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGC-ACGATATCC-TCTG
64 AACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGT--CTA--ATATCCTTC-G
* *
1037791 -TCGTGGAGTTGAAATCG-CGGATGAAACTGAAAATTTGTTCGTTGACAACCAACCGTCCCTTCG
124 CT-GTGAAGTTGAAATCGAC-GATG-AAC-G-AAA--TCTT-GTTGACAACCAACCGTCCCTTCG
*
1037854 TTGTGAAGTTGAACTTGTGTTGTCT
181 TTGTGAAGTTGAACTTGTGTTATCT
* * *
1037879 CGGGTAGCACGATATCCTCCGTCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAATTGTTTGTTG
1 CGAGT--C-CAATATCCTCCG-CGTGGAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTG
* *
1037944 ACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAATCCAATATCCTTCGCTG
62 ACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTTCGCTG
* * * * * ** * * **
1038009 TGAAGTTGAGATTG--GCT--CCGAAATTTCTTGTCGACAGTCAGCCGCCCCTTCACTGTGAAGT
127 TGAAGTTGAAATCGACGATGAACGAAA--TCTTGTTGACAACCAACCGTCCCTTCGTTGTGAAGT
* * *
1038070 TGAGCTTGTGCTGTCT
190 TGAACTTGTGTTATCT
* * * * * * *
1038086 TGGGTCCAATATCCTTCGCTGTGAAGTTGAGATTGGCTC--------CGAAATTGTTTGTCGACA
1 CGAGTCCAATATCCTCCGC-GTGGAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACA
** * * * * * *
1038143 GTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCCTTCGCTGTGA
65 ACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTTCGCTGTGA
* ** * * * *
1038208 AGTTGAAAT-TAGCCCTAAAACTGGGAAATTATTGTTGACAACCAGCCGTCCCTTCGTTGTAAAG
130 AGTTGAAATCGA-CGAT-GAAC---GAAA-TCTTGTTGACAACCAACCGTCCCTTCGTTGTGAAG
*
1038272 TTGAACTTGTGTTGTCT
189 TTGAACTTGTGTTATCT
1038289 CGAGTCCAATATCCT
1 CGAGTCCAATATCCT
1038304 TCGCTGTGAA
Statistics
Matches: 527, Mismatches: 80, Indels: 69
0.78 0.12 0.10
Matches are distributed among these distances:
196 81 0.15
198 2 0.00
201 1 0.00
203 57 0.11
204 32 0.06
205 1 0.00
206 93 0.18
207 44 0.08
208 13 0.02
209 23 0.04
210 4 0.01
211 1 0.00
212 3 0.01
213 2 0.00
214 3 0.01
215 67 0.13
216 4 0.01
217 2 0.00
218 90 0.17
219 2 0.00
220 2 0.00
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.33
Consensus pattern (205 bp):
CGAGTCCAATATCCTCCGCGTGGAGTTGAAATTGGCTCTGGAATTGGGAAATTGTTTGTTGACAA
CCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTTCGCTGTGAA
GTTGAAATCGACGATGAACGAAATCTTGTTGACAACCAACCGTCCCTTCGTTGTGAAGTTGAACT
TGTGTTATCT
Found at i:1038065 original size:55 final size:55
Alignment explanation
Indices: 1038000--1038171 Score: 160
Period size: 55 Copynumber: 3.3 Consensus size: 55
1037990 AATCCAATAT
1038000 CCTTCGCTGTGAAGTTGAGATTGGCTCCGAAATTTCTTGTCGACAGTCAGCCGCC
1 CCTTCGCTGTGAAGTTGAGATTGGCTCCGAAATTTCTTGTCGACAGTCAGCCGCC
* * * *
1038055 CCTTCACTGTGAAGTTGAGCTTGTGCT--G-----TCTTGGGTC--CAAT-A-----T
1 CCTTCGCTGTGAAGTTGAGATTG-GCTCCGAAATTTCTT--GTCGACAGTCAGCCGCC
1038098 CCTTCGCTGTGAAGTTGAGATTGGCTCCGAAATTGT-TTGTCGACAGTCAGCCGCC
1 CCTTCGCTGTGAAGTTGAGATTGGCTCCGAAATT-TCTTGTCGACAGTCAGCCGCC
1038153 CCTTCGCTGTGAAGTTGAG
1 CCTTCGCTGTGAAGTTGAG
1038172 CTTGTGCTGT
Statistics
Matches: 90, Mismatches: 8, Indels: 38
0.66 0.06 0.28
Matches are distributed among these distances:
42 3 0.03
43 21 0.23
44 1 0.01
47 3 0.03
48 1 0.01
49 12 0.13
50 2 0.02
51 3 0.03
54 1 0.01
55 40 0.44
56 3 0.03
ACGTcount: A:0.17, C:0.24, G:0.27, T:0.31
Consensus pattern (55 bp):
CCTTCGCTGTGAAGTTGAGATTGGCTCCGAAATTTCTTGTCGACAGTCAGCCGCC
Found at i:1038108 original size:43 final size:43
Alignment explanation
Indices: 1038055--1038213 Score: 131
Period size: 43 Copynumber: 3.4 Consensus size: 43
1038045 GTCAGCCGCC
*
1038055 CCTTCACTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATAT
1 CCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATAT
* ** * * *
1038098 CCTTCGCTGTGAAGTTGAGATTG-GCTCCGAAATTGTTTGTCGACAGTCAGCCGCC
1 CCTTCGCTGTGAAGTTGAGCTTGTGCT--G-TCTTG--GGTC--CAAT-A-----T
1038153 CCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATAT
1 CCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATAT
1038196 CCTTCGCTGTGAAGTTGA
1 CCTTCGCTGTGAAGTTGA
1038214 AATTAGCCCT
Statistics
Matches: 89, Mismatches: 13, Indels: 28
0.68 0.10 0.22
Matches are distributed among these distances:
42 3 0.03
43 39 0.44
44 1 0.01
45 3 0.03
47 3 0.03
48 1 0.01
49 6 0.07
50 1 0.01
51 3 0.03
53 3 0.03
54 1 0.01
55 22 0.25
56 3 0.03
ACGTcount: A:0.16, C:0.23, G:0.27, T:0.34
Consensus pattern (43 bp):
CCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATAT
Found at i:1038955 original size:65 final size:65
Alignment explanation
Indices: 1038851--1039016 Score: 305
Period size: 65 Copynumber: 2.6 Consensus size: 65
1038841 GACAAAATTT
1038851 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
1038916 TGTTTCAAGAGAAACTATCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
1038981 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATT
1039017 TTGTTTCGAG
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
65 97 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.31
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:1039022 original size:102 final size:101
Alignment explanation
Indices: 1038916--1039373 Score: 763
Period size: 102 Copynumber: 4.5 Consensus size: 101
1038906 TCAATGTTTA
*
1038916 TGTTTCAAGAGAAACTATCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGAC-AAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1038981 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
65 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
1039018 TGTTTCGAGGGAAACTATCTCAAGAGAGACACAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACA-AATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1039083 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
65 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
1039120 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGAC-AAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* **
1039185 TGTTTCAAGAGAAACTGTCTCAATGGAGACGGAATTT
65 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
1039222 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGAC-AAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
1039287 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
65 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* * **
1039324 TGTTTAAAGGGAAACTGTCTCAAGAGAGACAAAGTTTGTTTCAAGGGAAA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAA-TTCATTTCAAGGGAAA
1039374 CTGTCTCAAG
Statistics
Matches: 335, Mismatches: 18, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
101 4 0.01
102 330 0.99
103 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.30
Consensus pattern (101 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAATTCATTTCAAGGGAAATGTTTTCAATGTTTAT
GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:1039032 original size:37 final size:37
Alignment explanation
Indices: 1038981--1039391 Score: 251
Period size: 37 Copynumber: 11.9 Consensus size: 37
1038971 TCAATGTTTA
* *
1038981 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * *
1039018 TGTTTCGAGGGAAACTATCTCAAGAGAGACACAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * *
1039054 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* *
1039082 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
1039120 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * **
1039156 CATTTCAAGGGAAA-TGTTTC--------CAATGTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* **
1039184 ATGTTTCAAGAGAAACTGTCTCAATG-GAGACGGAATTT
1 -TGTTTCAAGGGAAACTGTCTCAA-GAGAGACAAAATTT
* *
1039222 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-CT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * *
1039258 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* * *
1039286 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* *
1039324 TGTTTAAAGGGAAACTGTCTCAAGAGAGAC-AAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
1039360 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1039392 TGGTGAGCAT
Statistics
Matches: 278, Mismatches: 57, Indels: 78
0.67 0.14 0.19
Matches are distributed among these distances:
27 3 0.01
28 5 0.02
29 39 0.14
30 11 0.04
32 2 0.01
33 2 0.01
34 2 0.01
35 8 0.03
36 81 0.29
37 115 0.41
38 10 0.04
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:1039106 original size:167 final size:169
Alignment explanation
Indices: 1038816--1039133 Score: 525
Period size: 167 Copynumber: 1.9 Consensus size: 169
1038806 AAGATGATGC
* *
1038816 TTCAAGAGAAAGTTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC
1 TTCAAGAGAAAGCTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
1038881 GAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
66 GAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
*
1038946 GAAA-TTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
131 AAAATTTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
* *
1038984 TTCAAGAGAAA-CTGTCTCAAGGGAGACAAAATTTTGTTTCGAGGGAAACTATCTCAAGAGAGAC
1 TTCAAGAGAAAGCTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
* *
1039048 -ACAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGA
66 GA-AATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGA
**
1039112 CAAAATTTTGTTTCAAGGGAAA
130 CAAAATTTCATTTCAAGGGAAA
1039134 CTATCTCAAG
Statistics
Matches: 139, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
166 1 0.01
167 113 0.81
168 25 0.18
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (169 bp):
TTCAAGAGAAAGCTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
GAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
AAAATTTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
Found at i:1039370 original size:36 final size:36
Alignment explanation
Indices: 1039287--1039391 Score: 156
Period size: 36 Copynumber: 2.9 Consensus size: 36
1039277 TCAATGTTTA
* * * *
1039287 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAG-ACAAAGTT
*
1039324 TGTTTAAAGGGAAACTGTCTCAAGAGAGACAAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTT
1039360 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1039392 TGGTGAGCAT
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
36 37 0.60
37 25 0.40
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTT
Found at i:1040275 original size:22 final size:22
Alignment explanation
Indices: 1040250--1040300 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1040240 TTGTGTTTGG
1040250 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
1040272 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
1040294 TCAAAGG
1 TCAAAGG
1040301 ATTGATGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:1040933 original size:20 final size:20
Alignment explanation
Indices: 1040908--1040967 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
1040898 TTTTTGTCCC
*
1040908 CTTTTTTATTTTTGTTCTTT
1 CTTTTTTATTCTTGTTCTTT
* *
1040928 CTTTTTTGTTCTTGTTTTTT
1 CTTTTTTATTCTTGTTCTTT
**
1040948 CCTTTTTGCTTCTT-TTCTTT
1 -CTTTTTTATTCTTGTTCTTT
1040968 TTTCTTTTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 22 0.67
21 11 0.33
ACGTcount: A:0.02, C:0.15, G:0.07, T:0.77
Consensus pattern (20 bp):
CTTTTTTATTCTTGTTCTTT
Found at i:1040985 original size:22 final size:23
Alignment explanation
Indices: 1040942--1040984 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1040932 TTTGTTCTTG
*
1040942 TTTTTTCCTTTTTGCTTCTTTTC
1 TTTTTTCCTTTTTGCCTCTTTTC
1040965 TTTTTT-CTTTTTGCC-CTTTT
1 TTTTTTCCTTTTTGCCTCTTTT
1040985 TGTTCTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 8 0.42
23 6 0.32
ACGTcount: A:0.00, C:0.21, G:0.05, T:0.74
Consensus pattern (23 bp):
TTTTTTCCTTTTTGCCTCTTTTC
Found at i:1045620 original size:2 final size:2
Alignment explanation
Indices: 1045615--1045652 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1045605 CATTATGATA
*
1045615 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AG AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1045653 ATAAGGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1045675 original size:21 final size:23
Alignment explanation
Indices: 1045641--1045700 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 23
1045631 ATATATATAT
*
1045641 ATAATAGATATAATAAGGAAAA-A
1 ATAATA-ATGTAATAAGGAAAATA
* *
1045664 A-AATAATTTAATAAAGTAAAATA
1 ATAATAATGTAAT-AAGGAAAATA
1045687 ATAATAATGTAATA
1 ATAATAATGTAATA
1045701 TAATATAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 6 0.19
22 11 0.35
23 4 0.13
24 10 0.32
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.28
Consensus pattern (23 bp):
ATAATAATGTAATAAGGAAAATA
Found at i:1045693 original size:16 final size:16
Alignment explanation
Indices: 1045672--1045709 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1045662 AAAAATAATT
1045672 TAATAAAGTAAAATAA
1 TAATAAAGTAAAATAA
* *
1045688 TAATAATGTAATATAA
1 TAATAAAGTAAAATAA
1045704 T-ATAAA
1 TAATAAA
1045710 TACATGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
TAATAAAGTAAAATAA
Found at i:1045800 original size:16 final size:15
Alignment explanation
Indices: 1045779--1045817 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1045769 TGCACATGTT
*
1045779 TAAAAAAAAGTAAAAA
1 TAAAAAAAAAT-AAAA
1045795 TAAAAATAAAATAAAA
1 TAAAAA-AAAATAAAA
1045811 TAAAAAA
1 TAAAAAA
1045818 TATACATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 16 0.76
17 4 0.19
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (15 bp):
TAAAAAAAAATAAAA
Found at i:1045914 original size:2 final size:2
Alignment explanation
Indices: 1045902--1045937 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1045892 ATATAATAGT
*
1045902 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1045938 ATAACTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1046464 original size:35 final size:37
Alignment explanation
Indices: 1046420--1046488 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
1046410 AACATAGCAA
1046420 AATTCTATCCT-ATTTT-AGGAG-TTGAATCCTAACAG
1 AATTCTATCCTAATTTTGA-GAGTTTGAATCCTAACAG
1046455 AATTCTATCCTAATTTTGAGAGTTTGAATCCTAA
1 AATTCTATCCTAATTTTGAGAGTTTGAATCCTAA
1046489 TAGGACGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
35 11 0.35
36 8 0.26
37 12 0.39
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (37 bp):
AATTCTATCCTAATTTTGAGAGTTTGAATCCTAACAG
Found at i:1049900 original size:22 final size:22
Alignment explanation
Indices: 1049869--1049911 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1049859 AAATTTTAGA
*
1049869 GAAACTGAAAGCAACCCGAACT
1 GAAACCGAAAGCAACCCGAACT
**
1049891 GAAACCGAAATTAACCCGAAC
1 GAAACCGAAAGCAACCCGAAC
1049912 CAACAAAAGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.28, G:0.16, T:0.09
Consensus pattern (22 bp):
GAAACCGAAAGCAACCCGAACT
Found at i:1050009 original size:187 final size:187
Alignment explanation
Indices: 1049694--1050032 Score: 572
Period size: 187 Copynumber: 1.8 Consensus size: 187
1049684 AACCAAAATT
*
1049694 AACCCGAACTGAAACCGAAATTAACCCAAACCAACAAAAGTAAGCCGAACCAAAACTAACCCGAA
1 AACCCGAACTGAAACCGAAATTAACCCAAACCAACAAAAGCAAGCCGAACCAAAACTAACCCGAA
* * ** *
1049759 CCGAAAGAAGCCCAAACCAAATTTCAAACCGTACCGAATTTTAACCTGATCTGAAAGCAACCTAA
66 CCGAAAGAAACCCAAACCAAATTTCAAACCGTACCGAATTTTAACCCGATCCAAAAACAACCTAA
*
1049824 ACCAAATTTAATCCGACCCGAACTATACCCAATCCAAATTTTAGAGAAACTGAAAGC
131 ACCAAATTTAACCCGACCCGAACTATACCCAATCCAAATTTTAGAGAAACTGAAAGC
*
1049881 AACCCGAACTGAAACCGAAATTAACCCGAACCAACAAAAGCAAGCCGAACCAAAACTAACCCGAA
1 AACCCGAACTGAAACCGAAATTAACCCAAACCAACAAAAGCAAGCCGAACCAAAACTAACCCGAA
* *
1049946 CTGAAAGAAACCCAAACCAAATTTC-AACATGTACCGAATTTTAACCCGATCCAAAAACAACCTA
66 CCGAAAGAAACCCAAACCAAATTTCAAAC-CGTACCGAATTTTAACCCGATCCAAAAACAACCTA
1050010 AACCAAATTTAACCCGACCCGAA
130 AACCAAATTTAACCCGACCCGAA
1050033 AGAAACCCAA
Statistics
Matches: 141, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
186 3 0.02
187 138 0.98
ACGTcount: A:0.46, C:0.29, G:0.11, T:0.14
Consensus pattern (187 bp):
AACCCGAACTGAAACCGAAATTAACCCAAACCAACAAAAGCAAGCCGAACCAAAACTAACCCGAA
CCGAAAGAAACCCAAACCAAATTTCAAACCGTACCGAATTTTAACCCGATCCAAAAACAACCTAA
ACCAAATTTAACCCGACCCGAACTATACCCAATCCAAATTTTAGAGAAACTGAAAGC
Found at i:1050064 original size:32 final size:32
Alignment explanation
Indices: 1049986--1050076 Score: 85
Period size: 32 Copynumber: 2.8 Consensus size: 32
1049976 GTACCGAATT
* * * * *
1049986 TTAACCCGATCC-AAAAACAACCTAAACCAAAT
1 TTAACCCGAACCGAAAGA-AACCCAAACAAAAA
*
1050018 TTAACCCGACCCGAAAGAAACCCAAACAAAAA
1 TTAACCCGAACCGAAAGAAACCCAAACAAAAA
* * *
1050050 TTAATCCGAACCGAAAGTAACTCAAAC
1 TTAACCCGAACCGAAAGAAACCCAAAC
1050077 CGAAAGCAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
32 45 0.92
33 4 0.08
ACGTcount: A:0.49, C:0.30, G:0.08, T:0.13
Consensus pattern (32 bp):
TTAACCCGAACCGAAAGAAACCCAAACAAAAA
Found at i:1050328 original size:14 final size:14
Alignment explanation
Indices: 1050305--1050334 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1050295 TTACATTGAG
1050305 TTTCTCAATAAAAC
1 TTTCTCAATAAAAC
*
1050319 TTTCTTAATAAAAC
1 TTTCTCAATAAAAC
1050333 TT
1 TT
1050335 AAAAGAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (14 bp):
TTTCTCAATAAAAC
Found at i:1050987 original size:17 final size:17
Alignment explanation
Indices: 1050959--1051001 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1050949 ACATTAAATG
*
1050959 AAAAATAGAAAAA-TATA
1 AAAAATAAAAAAAGT-TA
1050976 AAAAATAAAAAAAGTTA
1 AAAAATAAAAAAAGTTA
1050993 AAAATATAA
1 AAAA-ATAA
1051002 GAAACTTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.19
Consensus pattern (17 bp):
AAAAATAAAAAAAGTTA
Found at i:1053537 original size:17 final size:16
Alignment explanation
Indices: 1053511--1053549 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
1053501 AATTTAAACG
* *
1053511 ATAAAAATTATTTTGA
1 ATAAAAATTAATTTAA
1053527 ATAATAAATTAATTTAA
1 ATAA-AAATTAATTTAA
1053544 ATAAAA
1 ATAAAA
1053550 TTGGTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
ATAAAAATTAATTTAA
Found at i:1053953 original size:30 final size:30
Alignment explanation
Indices: 1053917--1053976 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
1053907 TACGAGATTA
1053917 ATGTAAAAATTTGATAACAAATTCTAACAC
1 ATGTAAAAATTTGATAACAAATTCTAACAC
* * *
1053947 ATGTAAAATTTTGATGAGAAATTCTAACAC
1 ATGTAAAAATTTGATAACAAATTCTAACAC
1053977 GTATTATAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.32
Consensus pattern (30 bp):
ATGTAAAAATTTGATAACAAATTCTAACAC
Found at i:1054301 original size:33 final size:32
Alignment explanation
Indices: 1054210--1054302 Score: 82
Period size: 33 Copynumber: 2.9 Consensus size: 32
1054200 ACCTAAACCG
* **
1054210 AAAATCAACTAATATGATATTGA-CTCGACCCG
1 AAAATCAACTGATATGATATTGATCT-GACCAA
* * * *
1054242 AAATTTAACCGAT-TCGATATTAATCTGACCAAA
1 AAAATCAACTGATAT-GATATTGATCTGACC-AA
1054275 AAAATCAACTGATATGATATTGATCTGA
1 AAAATCAACTGATATGATATTGATCTGA
1054303 ATCGAAAATC
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
31 1 0.02
32 20 0.43
33 24 0.52
34 1 0.02
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (32 bp):
AAAATCAACTGATATGATATTGATCTGACCAA
Found at i:1055888 original size:18 final size:18
Alignment explanation
Indices: 1055865--1055904 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
1055855 GGTTGGTACG
1055865 AATGGTAAGTCTGTACCA
1 AATGGTAAGTCTGTACCA
1055883 AATGGTAAGTCTGTACCA
1 AATGGTAAGTCTGTACCA
1055901 AATG
1 AATG
1055905 ATATGTATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.28
Consensus pattern (18 bp):
AATGGTAAGTCTGTACCA
Found at i:1058041 original size:39 final size:39
Alignment explanation
Indices: 1057979--1058061 Score: 114
Period size: 39 Copynumber: 2.1 Consensus size: 39
1057969 CATGCTTTTG
* *
1057979 ATCATGAATATGAGGGTCTTGTTGCTGATTCTATTGGCT
1 ATCATGAACATGAGGATCTTGTTGCTGATTCTATTGGCT
*
1058018 ATCATGAACATGAGGATAC-TGTTGCTGATTCTGTTGGCT
1 ATCATGAACATGAGGAT-CTTGTTGCTGATTCTATTGGCT
*
1058057 CTCAT
1 ATCAT
1058062 AATGGTCTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 38 0.97
40 1 0.03
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.39
Consensus pattern (39 bp):
ATCATGAACATGAGGATCTTGTTGCTGATTCTATTGGCT
Found at i:1065931 original size:6 final size:6
Alignment explanation
Indices: 1065920--1065951 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1065910 AAGAAAAGAT
1065920 GTGAAG GTGAAG GTGAAG GTGAAG GTGAAG GT
1 GTGAAG GTGAAG GTGAAG GTGAAG GTGAAG GT
1065952 AAAAAGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.50, T:0.19
Consensus pattern (6 bp):
GTGAAG
Found at i:1071271 original size:12 final size:12
Alignment explanation
Indices: 1071254--1071283 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
1071244 AAGAATATGA
1071254 AATAAGAGGTAT
1 AATAAGAGGTAT
1071266 AATAAGAGGTAT
1 AATAAGAGGTAT
1071278 AATAAG
1 AATAAG
1071284 GACATAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.23, T:0.23
Consensus pattern (12 bp):
AATAAGAGGTAT
Found at i:1071740 original size:32 final size:32
Alignment explanation
Indices: 1071660--1071747 Score: 99
Period size: 31 Copynumber: 2.8 Consensus size: 32
1071650 AGAGTTGAGG
* *
1071660 GTTACCTATGTCTTTT-GAGACATAAAGACAGT
1 GTTACCTATGT-TTTTCGAGACATATAGACAAT
* **
1071692 -TTACCTGTGTCATTCGAGACATATAGACAAT
1 GTTACCTATGTTTTTCGAGACATATAGACAAT
*
1071723 GTTACCTATGTTTTTCGAAACATAT
1 GTTACCTATGTTTTTCGAGACATAT
1071748 GGATAGGTCC
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
30 2 0.04
31 23 0.51
32 20 0.44
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (32 bp):
GTTACCTATGTTTTTCGAGACATATAGACAAT
Found at i:1072588 original size:18 final size:18
Alignment explanation
Indices: 1072565--1072609 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1072555 GCTTGAGATA
* *
1072565 ACCTAAAGAAAATAACAT
1 ACCTAAAGAAAATAAAAC
*
1072583 ACCTAAAGGAAATAAAAC
1 ACCTAAAGAAAATAAAAC
1072601 ACCTAAAGA
1 ACCTAAAGA
1072610 TTATCCTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.60, C:0.18, G:0.09, T:0.13
Consensus pattern (18 bp):
ACCTAAAGAAAATAAAAC
Found at i:1078953 original size:20 final size:20
Alignment explanation
Indices: 1078928--1079002 Score: 88
Period size: 20 Copynumber: 4.0 Consensus size: 20
1078918 TCGTTGCAGC
1078928 CAGGGTGTATGGATACACTG
1 CAGGGTGTATGGATACACTG
* *
1078948 CAGGGTGTATCGATATAC--
1 CAGGGTGTATGGATACACTG
1078966 CA--GTGTATGGATACACTG
1 CAGGGTGTATGGATACACTG
1078984 CAGGGTGTATCGG-TACACT
1 CAGGGTGTAT-GGATACACT
1079003 AATTACATTC
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
16 12 0.26
18 4 0.09
20 28 0.61
21 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (20 bp):
CAGGGTGTATGGATACACTG
Found at i:1079057 original size:20 final size:20
Alignment explanation
Indices: 1079032--1079123 Score: 81
Period size: 20 Copynumber: 4.8 Consensus size: 20
1079022 GTAGTCATAG
**
1079032 GGTGTATGGATACACTGTAT
1 GGTGTATGGATACACTACAT
1079052 GGTGTATGGATACACTACAT
1 GGTGTATGGATACACTACAT
1079072 GGTGTATTGG-TACAC--CA-
1 GGTGTA-TGGATACACTACAT
*
1079089 -GTGTATGGATACATTACA-
1 GGTGTATGGATACACTACAT
1079107 GAGTGTATCGG-TACACT
1 G-GTGTAT-GGATACACT
1079124 TTAGCATTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
15 3 0.05
16 9 0.15
18 4 0.07
20 40 0.66
21 5 0.08
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (20 bp):
GGTGTATGGATACACTACAT
Found at i:1079100 original size:36 final size:36
Alignment explanation
Indices: 1079053--1079122 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
1079043 ACACTGTATG
*
1079053 GTGTATGGATACACTACATG-GTGTATTGGTACACCA
1 GTGTATGGATACACTACA-GAGTGTATCGGTACACCA
*
1079089 GTGTATGGATACATTACAGAGTGTATCGGTACAC
1 GTGTATGGATACACTACAGAGTGTATCGGTACAC
1079123 TTTAGCATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 1 0.03
36 30 0.97
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.30
Consensus pattern (36 bp):
GTGTATGGATACACTACAGAGTGTATCGGTACACCA
Found at i:1079381 original size:18 final size:19
Alignment explanation
Indices: 1079336--1079392 Score: 64
Period size: 18 Copynumber: 3.0 Consensus size: 19
1079326 ATGTTTAATG
1079336 AAAAG-TATCAATTGTTAAC
1 AAAAGATATCAATTGTT-AC
1079355 AAAAGGATATCAATTGTTA-
1 AAAA-GATATCAATTGTTAC
* *
1079374 AAAAGATACCAAATGTTAC
1 AAAAGATATCAATTGTTAC
1079393 CAATTGTTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 12 0.36
19 8 0.24
20 2 0.06
21 11 0.33
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.28
Consensus pattern (19 bp):
AAAAGATATCAATTGTTAC
Found at i:1082386 original size:18 final size:19
Alignment explanation
Indices: 1082360--1082398 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
1082350 GAGATAAACT
*
1082360 AAAGAAAATAAAATACCTA
1 AAAGAAAATAAAACACCTA
1082379 AAAG-AAATAAAACACCTA
1 AAAGAAAATAAAACACCTA
1082397 AA
1 AA
1082399 GATAATCCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.69, C:0.13, G:0.05, T:0.13
Consensus pattern (19 bp):
AAAGAAAATAAAACACCTA
Found at i:1084298 original size:39 final size:39
Alignment explanation
Indices: 1084218--1084304 Score: 113
Period size: 39 Copynumber: 2.2 Consensus size: 39
1084208 AAGAAGATAT
*
1084218 TGATGATGACGACGACGATGAAGAAGACGAATTAGAAGA
1 TGATGATGACGACGACGATGAAGAAGACGAATGAGAAGA
* * * *
1084257 TGATGATGACGACGACGGTGGAGAAGACGGA-GACGATGA
1 TGATGATGACGACGACGATGAAGAAGACGAATGA-GAAGA
1084296 TGATGATGA
1 TGATGATGA
1084305 AGAAGAAGAG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
38 1 0.02
39 41 0.98
ACGTcount: A:0.38, C:0.10, G:0.36, T:0.16
Consensus pattern (39 bp):
TGATGATGACGACGACGATGAAGAAGACGAATGAGAAGA
Found at i:1085747 original size:20 final size:21
Alignment explanation
Indices: 1085722--1085773 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1085712 TTTTCCCAAT
*
1085722 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1085742 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1085763 TCGCAATGCGA
1 TCGCAATGCGA
1085774 TACTAACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1085790 original size:20 final size:20
Alignment explanation
Indices: 1085762--1085876 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
1085752 AATTGGGAAA
1085762 ATCGCAATGCGATACTAACT
1 ATCGCAATGCGATACTAACT
* *
1085782 ATCGTAATGCGATACTTACT
1 ATCGCAATGCGATACTAACT
* **
1085802 ATCGCAATGCGATAATACAAA
1 ATCGCAATGCGATACTA-ACT
* * *
1085823 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTAACT
* * *
1085843 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTAAC-T
1085863 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
1085877 TTTCAAAGCG
Statistics
Matches: 74, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
19 2 0.03
20 47 0.64
21 25 0.34
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTAACT
Found at i:1085824 original size:61 final size:62
Alignment explanation
Indices: 1085759--1085876 Score: 150
Period size: 61 Copynumber: 1.9 Consensus size: 62
1085749 GCGAATTGGG
* * * * *
1085759 AAAATCGCAATGCGATACTAACTATCGTAATGCGATACTTAC-T-ATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTAACTATCGCAACGCGATA-ATACATAATCGCAATGCGATAATAC
* *
1085820 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATAATACATAATCGCAATGCGAT
1 AAAATCGCAACGAGATACTAACTATCGCAACGCGATAATACATAATCGCAATGCGAT
1085877 TTTCAAAGCG
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
60 3 0.06
61 32 0.67
62 13 0.27
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (62 bp):
AAAATCGCAACGAGATACTAACTATCGCAACGCGATAATACATAATCGCAATGCGATAATAC
Found at i:1085849 original size:41 final size:41
Alignment explanation
Indices: 1085792--1085870 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
1085782 ATCGTAATGC
* *
1085792 GATACTTACTATCGCAATGCGATAATACAAAATCGCAACGA
1 GATACTGACTATCGCAACGCGATAATACAAAATCGCAACGA
* *
1085833 GATACTGACTTTCGCAACGCGATAATACATAATCGCAA
1 GATACTGACTATCGCAACGCGATAATACAAAATCGCAA
1085871 TGCGATTTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.23
Consensus pattern (41 bp):
GATACTGACTATCGCAACGCGATAATACAAAATCGCAACGA
Found at i:1086074 original size:22 final size:22
Alignment explanation
Indices: 1086046--1086087 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1086036 CTCTCTCACC
1086046 CATCTCCGACGAAATCCGTCCA
1 CATCTCCGACGAAATCCGTCCA
**
1086068 CATCTCCGGTGAAATCCGTC
1 CATCTCCGACGAAATCCGTC
1086088 TATCTCCATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.38, G:0.17, T:0.21
Consensus pattern (22 bp):
CATCTCCGACGAAATCCGTCCA
Found at i:1086404 original size:20 final size:20
Alignment explanation
Indices: 1086350--1086408 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1086340 GCGATTCTCT
**
1086350 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
1086370 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
1086390 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
1086409 AGAAACTATT
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:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1086596 original size:25 final size:24
Alignment explanation
Indices: 1086542--1086596 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1086532 TGTTTATTAT
* *
1086542 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1086566 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1086592 TGTTT
1 TGTTT
1086597 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1087746 original size:18 final size:18
Alignment explanation
Indices: 1087720--1087764 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1087710 CAACTTTCGG
*
1087720 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1087738 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1087756 GAGCCATCA
1 GAGCCATCA
1087765 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1088299 original size:18 final size:20
Alignment explanation
Indices: 1088257--1088300 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
1088247 CGCAACACGA
1088257 AAATGACTATCGCAATGCAG
1 AAATGACTATCGCAATGCAG
1088277 AAATG-CTATCGCAATGC-G
1 AAATGACTATCGCAATGCAG
1088295 AAATGA
1 AAATGA
1088301 AAATCGCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.26
19 12 0.52
20 5 0.22
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATGACTATCGCAATGCAG
Found at i:1088306 original size:19 final size:19
Alignment explanation
Indices: 1088265--1088379 Score: 83
Period size: 19 Copynumber: 6.6 Consensus size: 19
1088255 GAAAATGACT
**
1088265 ATCGCAATGCAGAAATG-CT
1 ATCGCAATGC-GAAATGAAA
1088284 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1088303 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
1088317 ATCGTAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
1088335 ATCGCAA--C--AA-CAAA
1 ATCGCAATGCGAAATGAAA
*
1088349 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1088368 ATCGCAATGCGA
1 ATCGCAATGCGA
1088380 TTTGTGTTTC
Statistics
Matches: 75, Mismatches: 9, Indels: 24
0.69 0.08 0.22
Matches are distributed among these distances:
14 20 0.27
15 1 0.01
16 4 0.05
17 2 0.03
18 17 0.23
19 31 0.41
ACGTcount: A:0.45, C:0.21, G:0.19, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1088319 original size:14 final size:14
Alignment explanation
Indices: 1088300--1088357 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
1088290 ATGCGAAATG
1088300 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
1088314 AAAATCGTAATGCGAA
1 AAAATCGCAA--CGAC
*
1088330 ATGAAATCGCAACAAC
1 A--AAATCGCAACGAC
1088346 AAAATCGCAACG
1 AAAATCGCAACG
1088358 CGAAATGAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
14 19 0.56
16 7 0.21
18 8 0.24
ACGTcount: A:0.50, C:0.22, G:0.16, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1088342 original size:32 final size:33
Alignment explanation
Indices: 1088284--1088374 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
1088274 CAGAAATGCT
*
1088284 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
*
1088317 ATCGTAATGCGAAATG-AAATCGCAACAACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACAACAAA
*
1088349 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
1088375 TGCGATTTGT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 29 0.55
33 24 0.45
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACAACAAA
Found at i:1088413 original size:14 final size:14
Alignment explanation
Indices: 1088391--1088448 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1088381 TTGTGTTTCG
*
1088391 CGTTCCGATTTTGT
1 CGTTGCGATTTTGT
*
1088405 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1088421 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1088437 CGTTGCGATTTT
1 CGTTGCGATTTT
1088449 TATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.10, C:0.19, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1088459 original size:33 final size:33
Alignment explanation
Indices: 1088375--1088467 Score: 134
Period size: 32 Copynumber: 2.8 Consensus size: 33
1088365 AAAATCGCAA
* * * *
1088375 TGCGATTTGTGTTTCGCGTTCCGATTTTGTCGT
1 TGCGATTTTTATTTCGCATTGCGATTTTGTCGT
*
1088408 TGCGA-TTTCATTTCGCATTGCGATTTTGTCGT
1 TGCGATTTTTATTTCGCATTGCGATTTTGTCGT
1088440 TGCGATTTTTATTTCGCATTGCGATTTT
1 TGCGATTTTTATTTCGCATTGCGATTTT
1088468 CATTTCGCAT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
32 27 0.51
33 26 0.49
ACGTcount: A:0.11, C:0.17, G:0.23, T:0.49
Consensus pattern (33 bp):
TGCGATTTTTATTTCGCATTGCGATTTTGTCGT
Found at i:1088463 original size:19 final size:19
Alignment explanation
Indices: 1088407--1088506 Score: 95
Period size: 19 Copynumber: 5.5 Consensus size: 19
1088397 GATTTTGTCG
1088407 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1088425 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
*
1088439 TTGCGATTTTTATTTCGCA
1 TTGCGATTTTCATTTCGCA
1088458 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*** *
1088477 TTGCGATAGCCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
1088497 TTGCGATTTT
1 TTGCGATTTT
1088507 AAGTTTCGTG
Statistics
Matches: 66, Mismatches: 10, Indels: 10
0.77 0.12 0.12
Matches are distributed among these distances:
14 6 0.09
15 3 0.05
16 4 0.06
17 4 0.06
18 9 0.14
19 30 0.45
20 10 0.15
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1088965 original size:41 final size:41
Alignment explanation
Indices: 1088869--1088976 Score: 108
Period size: 41 Copynumber: 2.6 Consensus size: 41
1088859 GACTCACCTG
* * * * *
1088869 TCATCTCTTAAGAGTCCCCTCCAATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGT-CCCTCCCACCGTTCAAGAGGCCACTA
* *
1088911 TCCTCCCTCAAGAGTCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCTCCCACCGTTCAAGAGGCCACTA
** *
1088952 TCATCGTTGAAGAGGTCCCTCCCAC
1 TCATCCCTCAAGA-GTCCCTCCCAC
1088977 AATTTCAGAG
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 31 0.57
42 23 0.43
ACGTcount: A:0.21, C:0.39, G:0.17, T:0.23
Consensus pattern (41 bp):
TCATCCCTCAAGAGTCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:1090392 original size:14 final size:14
Alignment explanation
Indices: 1090373--1090408 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1090363 ATTGTTTAAT
1090373 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1090387 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1090401 TGATTTGT
1 TGATTTGT
1090409 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1090554 original size:14 final size:14
Alignment explanation
Indices: 1090535--1090588 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
1090525 GAAACTGACT
1090535 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
1090549 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
1090568 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
1090582 ATCGCAA
1 ATCGCAA
1090589 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:1090637 original size:20 final size:20
Alignment explanation
Indices: 1090620--1090707 Score: 115
Period size: 20 Copynumber: 4.4 Consensus size: 20
1090610 CGATTTTCTA
1090620 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
** *
1090640 GTTGCGATTTTCCA-TTTCGA
1 GTTGCGA-TAGCCATTTTCGC
*
1090660 ATTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
*
1090680 GTTGCGATAGACATTTTCGC
1 GTTGCGATAGCCATTTTCGC
1090700 GTTGCGAT
1 GTTGCGAT
1090708 TTCCCCATTG
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
19 4 0.07
20 49 0.86
21 4 0.07
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:1090645 original size:34 final size:37
Alignment explanation
Indices: 1090600--1090687 Score: 110
Period size: 40 Copynumber: 2.4 Consensus size: 37
1090590 GCGATTTTCA
* *
1090600 TTTCGCATTGCGATTTT-C-T-AGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCCTTCAATTGCGATAGCCAT
1090634 TTTCGCGTTGCGATTTTCCATTTCGAATTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCC--TTC-AATTGCGATAGCCAT
1090674 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
1090688 AGACATTTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
34 16 0.35
35 1 0.02
38 1 0.02
40 28 0.61
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.41
Consensus pattern (37 bp):
TTTCGCGTTGCGATTTTCCTTCAATTGCGATAGCCAT
Done.