Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002663.1 Hibiscus syriacus cultivar Beakdansim tig00005465_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: 975815
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 4 of 4
Found at i:830690 original size:12 final size:12
Alignment explanation
Indices: 830673--830705 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
830663 ATATAATCCT
830673 GAAGAAGAAAAA
1 GAAGAAGAAAAA
830685 GAAGAAGAAAAA
1 GAAGAAGAAAAA
830697 GAAGAAGAA
1 GAAGAAGAA
830706 GAAAAAGTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:833041 original size:14 final size:14
Alignment explanation
Indices: 833022--833076 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
833012 GCGAAATGAA
833022 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
833036 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
833055 AATCGCAACGAGAG
1 AATCGCAACGAGAG
833069 AATCGCAA
1 AATCGCAA
833077 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:833046 original size:33 final size:33
Alignment explanation
Indices: 833004--833161 Score: 264
Period size: 33 Copynumber: 4.8 Consensus size: 33
832994 GGAAATTACT
833004 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
833037 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
833070 ATCGCAATGCGAAATGAAAATCGCAACGCGA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
833102 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
833136 ATCGTAATGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
833162 TGCGAAATAA
Statistics
Matches: 117, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
32 1 0.01
33 115 0.98
34 1 0.01
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:833204 original size:19 final size:19
Alignment explanation
Indices: 833182--833223 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
833172 AAATCGCAAC
833182 GCGAATTTAATTTCGCGTT
1 GCGAATTTAATTTCGCGTT
* * *
833201 GCGATTTTCATTTCTCGTT
1 GCGAATTTAATTTCGCGTT
833220 GCGA
1 GCGA
833224 TTCTCTCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (19 bp):
GCGAATTTAATTTCGCGTT
Found at i:833224 original size:19 final size:19
Alignment explanation
Indices: 833191--833257 Score: 63
Period size: 19 Copynumber: 3.8 Consensus size: 19
833181 CGCGAATTTA
*
833191 ATTTCGCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
* *
833210 ATTTCTCGTTGCGA--TTC
1 ATTTCGCATTGCGATTTTC
*
833227 ---TCTCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
833243 ATTTCGCATTGCGAT
1 ATTTCGCATTGCGAT
833258 AGTACTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 10 0.25
16 3 0.08
17 3 0.08
19 24 0.60
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:834810 original size:21 final size:21
Alignment explanation
Indices: 834744--834810 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
834734 GTGAATCGGG
*
834744 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
834764 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
834786 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
834807 CTCT
1 CTCT
834811 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:834829 original size:42 final size:41
Alignment explanation
Indices: 834744--834866 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
834734 GTGAATCGGG
* * * *
834744 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
834786 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
834828 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
834867 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:835260 original size:91 final size:90
Alignment explanation
Indices: 835084--835268 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
835074 ATTTCAAACT
*
835084 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
835149 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
835177 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
* *
835241 GTATTGGCAGCAACTGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
835268 T
1 T
835269 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 41 0.47
93 19 0.22
95 27 0.31
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:836955 original size:20 final size:20
Alignment explanation
Indices: 836925--836984 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
836915 CTTTTGGTTG
*
836925 AAATGAAAATCGCAACGAGA
1 AAATGATAATCGCAACGAGA
* *
836945 TAATGATAATCGCAACGCGA
1 AAATGATAATCGCAACGAGA
836965 AAATGACT-ATCGCAACGAGA
1 AAATGA-TAATCGCAACGAGA
836985 GAATCGCAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 33 0.97
21 1 0.03
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (20 bp):
AAATGATAATCGCAACGAGA
Found at i:836992 original size:14 final size:14
Alignment explanation
Indices: 836973--837028 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
836963 GAAAATGACT
836973 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
836987 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
837004 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
837020 ATCGCAACG
1 ATCGCAACG
837029 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 6 0.17
19 7 0.20
ACGTcount: A:0.39, C:0.25, G:0.25, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:837007 original size:33 final size:33
Alignment explanation
Indices: 836952--837045 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
836942 AGATAATGAT
836952 AATCGCAACGCGAAAATGACTATCGCAACGAGAG
1 AATCGCAACGCG-AAATGACTATCGCAACGAGAG
836986 AATCGCAACGCGAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGAAATGACTATCGCAACGAGAG
**
837019 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGACTATCGCAA
837046 TGCGATTTTG
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 46 0.79
34 12 0.21
ACGTcount: A:0.43, C:0.23, G:0.22, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGACTATCGCAACGAGAG
Found at i:837062 original size:19 final size:19
Alignment explanation
Indices: 837046--837092 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
837036 AAAATCGCAA
*
837046 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
837065 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
837084 TGCGATTTT
1 TGCGATTTT
837093 CATTCTCGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.09, C:0.15, G:0.26, T:0.51
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:837652 original size:20 final size:19
Alignment explanation
Indices: 837611--837664 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
837601 GCTATGTAAA
*
837611 TCGCATTGCGATAGTAAGAT
1 TCGCATTGCGAT-TTAAGAT
*
837631 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTAAG-AT
*
837651 TCGCGTTGCGATTT
1 TCGCATTGCGATTT
837665 TCATAATTCG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 3 0.10
20 27 0.90
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (19 bp):
TCGCATTGCGATTTAAGAT
Found at i:837675 original size:21 final size:20
Alignment explanation
Indices: 837611--837676 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
837601 GCTATGTAAA
* *
837611 TCGCATTGCGATAGTA-AGAT
1 TCGCATTGCGAT-TTACATAT
*
837631 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACATAT
* *
837651 TCGCGTTGCGATTTTCATAAT
1 TCGCATTGCGATTTACAT-AT
837672 TCGCA
1 TCGCA
837677 AATCGCAATG
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
19 2 0.05
20 29 0.78
21 6 0.16
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:837842 original size:21 final size:21
Alignment explanation
Indices: 837802--837842 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
837792 ACTGTAGACC
** *
837802 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
837823 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
837843 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:840000 original size:22 final size:22
Alignment explanation
Indices: 839975--840019 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
839965 CCCTACCTCC
839975 TCTTACTTAATTAAAAATAAGA
1 TCTTACTTAATTAAAAATAAGA
839997 TCTTACTTAATTAAAAATAAGA
1 TCTTACTTAATTAAAAATAAGA
840019 T
1 T
840020 TTTGTTGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (22 bp):
TCTTACTTAATTAAAAATAAGA
Found at i:843936 original size:31 final size:31
Alignment explanation
Indices: 843889--843977 Score: 108
Period size: 31 Copynumber: 2.8 Consensus size: 31
843879 ATCGCATAAT
*
843889 GTTTACCTTTTT-TTTCATTTTAGTACCCGGC
1 GTTTA-CTTTTTGTTTCATTTTAGTACCCAGC
* **
843920 GTTTACTTTTTGTTTCATTTTAGTAACCATT
1 GTTTACTTTTTGTTTCATTTTAGTACCCAGC
*
843951 GTTAACTTTTTTGTTTCATTTTAGTAC
1 GTTTAC-TTTTTGTTTCATTTTAGTAC
843978 TTAATTTTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
30 6 0.12
31 25 0.50
32 19 0.38
ACGTcount: A:0.17, C:0.16, G:0.11, T:0.56
Consensus pattern (31 bp):
GTTTACTTTTTGTTTCATTTTAGTACCCAGC
Found at i:852124 original size:3 final size:3
Alignment explanation
Indices: 852116--852170 Score: 83
Period size: 3 Copynumber: 18.3 Consensus size: 3
852106 ACGTTTTAAA
* * *
852116 ATT ATT ATT ATT ATT ATT ATT ATA AAT ATT ATT ATT ATT ATT ATT AGT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
852164 ATT ATT A
1 ATT ATT A
852171 AATAAAATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:854386 original size:18 final size:19
Alignment explanation
Indices: 854357--854394 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
854347 TTAGGAAAAA
854357 TTATTATATTTTTAAATAT
1 TTATTATATTTTTAAATAT
*
854376 TTATT-TATTTTTTAATAT
1 TTATTATATTTTTAAATAT
854394 T
1 T
854395 AAAATTGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTATATTTTTAAATAT
Found at i:856841 original size:60 final size:60
Alignment explanation
Indices: 856729--856844 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
856719 CTCCACGATG
* * * *
856729 TCGACATTTAGGTCGAACAAGCTGGTAGTTGCATGTCTTCCCCTTGAACTTGAAGGCATC
1 TCGACATTGAGGTCGAACAAGCTGGCAGTTGAATGTCCTCCCCTTGAACTTGAAGGCATC
* * * *
856789 TCGACATTGAGGTCGAAGAAGCTTGCAGTTGAATG-CCTCCTCTTGGAGCTTGAAGG
1 TCGACATTGAGGTCGAACAAGCTGGCAGTTGAATGTCCTCCCCTT-GAACTTGAAGG
856845 AATCGTGTCA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
59 7 0.15
60 40 0.85
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (60 bp):
TCGACATTGAGGTCGAACAAGCTGGCAGTTGAATGTCCTCCCCTTGAACTTGAAGGCATC
Found at i:860002 original size:56 final size:55
Alignment explanation
Indices: 859916--860033 Score: 218
Period size: 56 Copynumber: 2.1 Consensus size: 55
859906 TAGCTAGTTT
859916 ATTATTATAATAATATTTTCTCCGGTTGAGCAAGAAAAAAAATATATTGTTGATTG
1 ATTATTATAATAATATTTTCTCCGGTTGAGCAAG-AAAAAAATATATTGTTGATTG
859972 ATTATTATAATAATATTTTCTCCGGTTGAGCAAGAAAAAAATATATTGTTGATTG
1 ATTATTATAATAATATTTTCTCCGGTTGAGCAAGAAAAAAATATATTGTTGATTG
860027 ATGTATT
1 AT-TATT
860034 TTGATGAAGA
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
55 23 0.38
56 38 0.62
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (55 bp):
ATTATTATAATAATATTTTCTCCGGTTGAGCAAGAAAAAAATATATTGTTGATTG
Found at i:862956 original size:15 final size:16
Alignment explanation
Indices: 862938--862967 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
862928 TTTTAATTAT
862938 ATTTAT-AATTAAAAG
1 ATTTATGAATTAAAAG
862953 ATTTATGAATTAAAA
1 ATTTATGAATTAAAA
862968 AACTATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (16 bp):
ATTTATGAATTAAAAG
Found at i:864172 original size:2 final size:2
Alignment explanation
Indices: 864160--864209 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
864150 TTATTCGATA
864160 AT AT A- 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
864201 AT AT AT AT A
1 AT AT AT AT A
864210 ATTGTACTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:864385 original size:3 final size:3
Alignment explanation
Indices: 864377--864421 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
864367 CATGCTGTTG
864377 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
864422 AGATCTAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:865212 original size:17 final size:17
Alignment explanation
Indices: 865185--865223 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
865175 AATTTACAAT
865185 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
865201 TAATTATAAATAATATC
1 TAATTATAAATAATATC
865218 TAATTA
1 TAATTA
865224 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:871206 original size:19 final size:21
Alignment explanation
Indices: 871182--871221 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
871172 TTTTATGTTG
871182 ATTCA-GAT-GTTGGATTTAT
1 ATTCAGGATCGTTGGATTTAT
*
871201 ATTCAGGTTCGTTGGATTTAT
1 ATTCAGGATCGTTGGATTTAT
871222 GTCTCTTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 2 0.11
21 11 0.61
ACGTcount: A:0.23, C:0.07, G:0.23, T:0.47
Consensus pattern (21 bp):
ATTCAGGATCGTTGGATTTAT
Found at i:872240 original size:24 final size:24
Alignment explanation
Indices: 872208--872257 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
872198 TATTGTGCCA
872208 CCTTATTAACACTAAACGAAATAT
1 CCTTATTAACACTAAACGAAATAT
872232 CCTTATTAACACTAAACGAAATAT
1 CCTTATTAACACTAAACGAAATAT
872256 CC
1 CC
872258 GGATGTGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.44, C:0.24, G:0.04, T:0.28
Consensus pattern (24 bp):
CCTTATTAACACTAAACGAAATAT
Found at i:878565 original size:41 final size:44
Alignment explanation
Indices: 878474--878569 Score: 117
Period size: 45 Copynumber: 2.2 Consensus size: 44
878464 AAATAATAAT
*
878474 TATTAATTTATTAATAAATAATAAAAAAATAATAAGTTAACTAATC
1 TATT-ATTTTTTAATAAATAATAAAAAAATAATAAGTTAACTAA-C
* * *
878520 TATTATTTTTTAATAAATAATAAAATATTATTAA-TTAAC-AA-
1 TATTATTTTTTAATAAATAATAAAAAAATAATAAGTTAACTAAC
878561 TATTATTTT
1 TATTATTTT
878570 AATACCAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
41 9 0.20
43 2 0.04
44 5 0.11
45 26 0.57
46 4 0.09
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (44 bp):
TATTATTTTTTAATAAATAATAAAAAAATAATAAGTTAACTAAC
Found at i:878752 original size:34 final size:31
Alignment explanation
Indices: 878660--878770 Score: 119
Period size: 31 Copynumber: 3.7 Consensus size: 31
878650 TTTAGTGAAC
* *
878660 TTAACGAGCAACGAGTTGAGCAGCAAATTTT
1 TTAACGAGCAACGAGTCGAGCAGCAAAATTT
878691 TTAACGAGC-ACGAGTCGAG-A-C--AA-TT
1 TTAACGAGCAACGAGTCGAGCAGCAAAATTT
878716 TTAACGAGCTTAACGAGTCGAGCAGCAAAAATTT
1 TTAACGAGC--AACGAGTCGAGCAGC-AAAATTT
*
878750 TTAACGAACAA-GAGTCGAGCA
1 TTAACGAGCAACGAGTCGAGCA
878771 ATACCCAACT
Statistics
Matches: 68, Mismatches: 3, Indels: 18
0.76 0.03 0.20
Matches are distributed among these distances:
25 11 0.16
26 1 0.01
28 11 0.16
29 2 0.03
30 10 0.15
31 19 0.28
32 2 0.03
33 2 0.03
34 10 0.15
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.22
Consensus pattern (31 bp):
TTAACGAGCAACGAGTCGAGCAGCAAAATTT
Found at i:878767 original size:59 final size:55
Alignment explanation
Indices: 878660--878772 Score: 154
Period size: 59 Copynumber: 2.0 Consensus size: 55
878650 TTTAGTGAAC
* * * *
878660 TTAACGAGCAACGAGTTGAGCAGCAAATTTTTTAACGAGCACGAGTCGAGACAATT
1 TTAACGAGCAACGAGTCGAGCAGCAAAATTTTTAACGAACAAGAGTCGAG-CAATT
878716 TTAACGAGCTTAACGAGTCGAGCAGCAAAAATTTTTAACGAACAAGAGTCGAGCAAT
1 TTAACGAGC--AACGAGTCGAGCAGC-AAAATTTTTAACGAACAAGAGTCGAGCAAT
878773 ACCCAACTCG
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
56 9 0.18
58 18 0.36
59 23 0.46
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (55 bp):
TTAACGAGCAACGAGTCGAGCAGCAAAATTTTTAACGAACAAGAGTCGAGCAATT
Found at i:880295 original size:2 final size:2
Alignment explanation
Indices: 880288--880322 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
880278 GAATCATGTG
880288 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
880323 CAGTTTCTTG
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:881990 original size:21 final size:21
Alignment explanation
Indices: 881966--882009 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
881956 AAATTACGCA
*
881966 TTCAGTAGCTAAACTATTAAT
1 TTCAGTACCTAAACTATTAAT
*
881987 TTCAGTACCTAAACTTTTAAT
1 TTCAGTACCTAAACTATTAAT
882008 TT
1 TT
882010 TTCCAAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.43
Consensus pattern (21 bp):
TTCAGTACCTAAACTATTAAT
Found at i:882229 original size:8 final size:8
Alignment explanation
Indices: 882216--882255 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
882206 TAACTTTCAA
882216 ATTTTTTT
1 ATTTTTTT
882224 ATTTTTTT
1 ATTTTTTT
*
882232 A---TTAT
1 ATTTTTTT
882237 ATTTTTTT
1 ATTTTTTT
882245 ATTTTTTT
1 ATTTTTTT
882253 ATT
1 ATT
882256 ATATATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
5 4 0.15
8 23 0.85
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.82
Consensus pattern (8 bp):
ATTTTTTT
Found at i:882241 original size:13 final size:13
Alignment explanation
Indices: 882223--882247 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
882213 CAAATTTTTT
882223 TATTTTTTTATTA
1 TATTTTTTTATTA
882236 TATTTTTTTATT
1 TATTTTTTTATT
882248 TTTTTATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TATTTTTTTATTA
Found at i:882242 original size:21 final size:21
Alignment explanation
Indices: 882216--882259 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
882206 TAACTTTCAA
882216 ATTTTTTTATTTTTTTATTAT
1 ATTTTTTTATTTTTTTATTAT
882237 ATTTTTTTATTTTTTTATTAT
1 ATTTTTTTATTTTTTTATTAT
882258 AT
1 AT
882260 ATTAATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (21 bp):
ATTTTTTTATTTTTTTATTAT
Found at i:882628 original size:14 final size:13
Alignment explanation
Indices: 882565--882631 Score: 64
Period size: 15 Copynumber: 4.8 Consensus size: 13
882555 TTACCTTAAA
882565 TTTTAAAGTATAAT
1 TTTTAAA-TATAAT
882579 TATTTAAATAT-AT
1 T-TTTAAATATAAT
*
882592 TTTTAAAAATTAAAT
1 TTTTAAATA-T-AAT
*
882607 TTTAAAATATAAT
1 TTTTAAATATAAT
882620 TATTTAAATATA
1 T-TTTAAATATA
882632 GGGTTTGCTA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
12 7 0.16
13 8 0.18
14 14 0.32
15 15 0.34
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (13 bp):
TTTTAAATATAAT
Found at i:882998 original size:31 final size:31
Alignment explanation
Indices: 882956--883019 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
882946 TTCATCCTAC
*
882956 TAGGCATTAGACCATGTTGATTTTTTATCAT
1 TAGGCACTAGACCATGTTGATTTTTTATCAT
882987 TAGGCACTAGACCATGTTGATTTTTTATCAT
1 TAGGCACTAGACCATGTTGATTTTTTATCAT
883018 TA
1 TA
883020 TGAATTCTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.44
Consensus pattern (31 bp):
TAGGCACTAGACCATGTTGATTTTTTATCAT
Found at i:883255 original size:29 final size:29
Alignment explanation
Indices: 883190--883259 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 29
883180 AGTGTGGCCA
*
883190 TGTCCCCC-AAAATTAAAAAAATTATAATT
1 TGTCCCCCTAAATTTAAAAAAA-TATAATT
* *
883219 TAGACCCCTTAAATTTAAAAAAA-ATAATT
1 T-GTCCCCCTAAATTTAAAAAAATATAATT
883248 TGTCCCCCTAAA
1 TGTCCCCCTAAA
883260 ATTTTTAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
28 9 0.26
29 8 0.24
30 5 0.15
31 12 0.35
ACGTcount: A:0.46, C:0.20, G:0.04, T:0.30
Consensus pattern (29 bp):
TGTCCCCCTAAATTTAAAAAAATATAATT
Found at i:883261 original size:29 final size:30
Alignment explanation
Indices: 883190--883263 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 30
883180 AGTGTGGCCA
883190 TGTCCCCC-AAAA-TTAAAAAAATTATAATT
1 TGTCCCCCTAAAATTTAAAAAAA-TATAATT
* *
883219 TAG-ACCCCTTAAATTTAAAAAAA-ATAATT
1 T-GTCCCCCTAAAATTTAAAAAAATATAATT
883248 TGTCCCCCTAAAATTT
1 TGTCCCCCTAAAATTT
883264 TTAAAAACTC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
28 1 0.03
29 23 0.62
30 4 0.11
31 9 0.24
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.32
Consensus pattern (30 bp):
TGTCCCCCTAAAATTTAAAAAAATATAATT
Found at i:884217 original size:27 final size:27
Alignment explanation
Indices: 884181--884235 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
884171 AAAAATTGAG
*
884181 TTTTCTTTTAAAAATATATTTT-TAAAT
1 TTTTATTTTAAAAATAT-TTTTCTAAAT
*
884208 TTTTATTTTAAATATATTTTTCTAAAT
1 TTTTATTTTAAAAATATTTTTCTAAAT
884235 T
1 T
884236 ATCGGAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (27 bp):
TTTTATTTTAAAAATATTTTTCTAAAT
Found at i:887724 original size:2 final size:2
Alignment explanation
Indices: 887719--887763 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
887709 TTAAAAAAAT
887719 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
887760 TA TA
1 TA TA
887764 ATAAAAGAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:888687 original size:2 final size:2
Alignment explanation
Indices: 888680--888704 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
888670 AATATTCTAT
888680 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 T
888705 TATGGTTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:894139 original size:17 final size:17
Alignment explanation
Indices: 894112--894150 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
894102 AATTTACAAT
*
894112 TAATT-TAAATAATATC
1 TAATTATAAATAATAGC
894128 TAATTATAAATAATAGC
1 TAATTATAAATAATAGC
894145 TAATTA
1 TAATTA
894151 ATTTGATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (17 bp):
TAATTATAAATAATAGC
Found at i:895323 original size:14 final size:14
Alignment explanation
Indices: 895287--895339 Score: 79
Period size: 14 Copynumber: 3.7 Consensus size: 14
895277 TAAAATTAAA
*
895287 ATTATTGTTATTAT
1 ATTATTATTATTAT
*
895301 AAATATTATTATTAT
1 -ATTATTATTATTAT
895316 ATTATTATTATTAT
1 ATTATTATTATTAT
895330 ATTATTATTA
1 ATTATTATTA
895340 AATAATTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
14 23 0.66
15 12 0.34
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
ATTATTATTATTAT
Found at i:895339 original size:11 final size:11
Alignment explanation
Indices: 895303--895337 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
895293 GTTATTATAA
895303 ATATTATTATT
1 ATATTATTATT
895314 ATATTATTATT
1 ATATTATTATT
895325 AT-TATATTATT
1 ATAT-TATTATT
895336 AT
1 AT
895338 TAAATAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 1 0.04
11 22 0.96
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
ATATTATTATT
Found at i:895347 original size:14 final size:13
Alignment explanation
Indices: 895262--895350 Score: 71
Period size: 14 Copynumber: 7.0 Consensus size: 13
895252 TTCATTTTAC
895262 TTAAATTATTATTA
1 TTAAA-TATTATTA
**
895276 TTAAA-ATTAAAA
1 TTAAATATTATTA
* *
895288 TT-ATTGTTATTA
1 TTAAATATTATTA
895300 -TAAATATTATTA
1 TTAAATATTATTA
895312 TT--ATATTATTA
1 TTAAATATTATTA
*
895323 TTATTATATTATTA
1 TTA-AATATTATTA
895337 TTAAATAATTATTA
1 TTAAAT-ATTATTA
895351 CAAACCCAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
11 13 0.22
12 19 0.32
13 3 0.05
14 24 0.41
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (13 bp):
TTAAATATTATTA
Found at i:895350 original size:3 final size:3
Alignment explanation
Indices: 895266--895339 Score: 71
Period size: 3 Copynumber: 25.3 Consensus size: 3
895256 TTTTACTTAA
** ** * * *
895266 ATT ATT ATT ATT AAA ATT AAA ATT ATT GTT ATT ATA AAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
895314 A-T ATT ATT ATT ATT A-T ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
895340 AATAATTATT
Statistics
Matches: 55, Mismatches: 14, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
2 4 0.07
3 51 0.93
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:895786 original size:13 final size:13
Alignment explanation
Indices: 895768--895792 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
895758 GAGAACGACA
895768 AAAAAAAAAACAG
1 AAAAAAAAAACAG
895781 AAAAAAAAAACA
1 AAAAAAAAAACA
895793 AAGCAAGAGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.08, G:0.04, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAACAG
Found at i:896047 original size:13 final size:13
Alignment explanation
Indices: 896029--896057 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
896019 ACCACCGTTA
896029 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
896042 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
896055 CGG
1 CGG
896058 AGTACGTGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:896642 original size:19 final size:19
Alignment explanation
Indices: 896604--896641 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
896594 TATAATTTAG
896604 TCATTTATTTTATATGTTT
1 TCATTTATTTTATATGTTT
896623 TCATTTATTTTAT-TGTTT
1 TCATTTATTTTATATGTTT
896641 T
1 T
896642 TAAAATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.71
Consensus pattern (19 bp):
TCATTTATTTTATATGTTT
Found at i:901186 original size:4 final size:4
Alignment explanation
Indices: 901177--901221 Score: 74
Period size: 4 Copynumber: 11.2 Consensus size: 4
901167 TTGTGCAAAA
901177 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA- ATAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT A
901222 TGTATTGCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 1 0.03
4 37 0.95
5 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:904537 original size:83 final size:83
Alignment explanation
Indices: 904435--904701 Score: 428
Period size: 83 Copynumber: 3.2 Consensus size: 83
904425 TAAATGGAAC
*
904435 AAATGAATATGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAA
1 AAATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAA
904500 CCAATCATTGAATTTGGA
66 CCAATCATTGAATTTGGA
* *
904518 AAATGAATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAA
1 AAATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAA
*
904583 CCAATCATTGAATTTAGA
66 CCAATCATTGAATTTGGA
* * * *
904601 AGATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGG-TTGGACAGA
1 AAATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAAA
*
904665 ACCAAGCATTGAATTTGGA
65 ACCAATCATTGAATTTGGA
*
904684 AGATGAATTTGCTCATAG
1 AAATGAATTTGCTCATAG
904702 TAGAAATAAG
Statistics
Matches: 171, Mismatches: 12, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
82 4 0.02
83 167 0.98
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (83 bp):
AAATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAA
CCAATCATTGAATTTGGA
Found at i:907338 original size:22 final size:22
Alignment explanation
Indices: 907307--907361 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
907297 ATCTACACTC
*
907307 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
907329 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
907351 TTCAAAGATGA
1 TTCAAAGATGA
907362 AAGCTTTATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:908148 original size:76 final size:76
Alignment explanation
Indices: 908022--909192 Score: 2119
Period size: 76 Copynumber: 15.4 Consensus size: 76
908012 CTATTTCCCA
*
908022 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
908087 AGCCTTCGGGT
66 AGCCTTCGGGT
*
908098 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
908163 AGCCTTCGGGT
66 AGCCTTCGGGT
908174 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
908239 ATCCTCCGGGT
66 AGCCTTCGGGT
908250 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
908315 ATCCTTCGGGT
66 AGCCTTCGGGT
*
908326 CATCTGTAAGCCCTTCAGTTCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
908391 ATCCTTCGGGT
66 AGCCTTCGGGT
*
908402 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGTAGCTTTTTGATGTTTTCA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
908467 AAGCCTTCGGGT
65 AAGCCTTCGGGT
908479 CATCTGTAAGCCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
908543 AGCCTTCGGGT
66 AGCCTTCGGGT
*
908554 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
908619 AGCCTTCGGGT
66 AGCCTTCGGGT
*
908630 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
908695 ATCCTTCGGGT
66 AGCCTTCGGGT
908706 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
908771 ATCCTTCGGGT
66 AGCCTTCGGGT
*
908782 CATCTGTAAGCCCTTCAGTTCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
908847 ATCCTTCGGGT
66 AGCCTTCGGGT
*
908858 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGTAGCTTTTTGATGTTTTCA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
908923 AAGCCTTCGGGT
65 AAGCCTTCGGGT
908935 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
909000 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
909011 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGTAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
909076 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
909087 CATCTGTAAGCCCTTCCGTGCATGATGTTTCCAAAAAGCATTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
909152 ATCCTTCGGGT
66 AGCCTTCGGGT
* *
909163 CATCTGTAAGTCCTGCAGTGCATGATGTTT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTT
909193 TTAAGACCTC
Statistics
Matches: 1065, Mismatches: 27, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
75 73 0.07
76 844 0.79
77 148 0.14
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:909403 original size:14 final size:14
Alignment explanation
Indices: 909367--909419 Score: 79
Period size: 14 Copynumber: 3.7 Consensus size: 14
909357 TAAAATTAAA
*
909367 ATTATTGTTATTAT
1 ATTATTATTATTAT
*
909381 AAATATTATTATTAT
1 -ATTATTATTATTAT
909396 ATTATTATTATTAT
1 ATTATTATTATTAT
909410 ATTATTATTA
1 ATTATTATTA
909420 AATAATTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
14 23 0.66
15 12 0.34
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
ATTATTATTATTAT
Found at i:909419 original size:11 final size:11
Alignment explanation
Indices: 909383--909417 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
909373 GTTATTATAA
909383 ATATTATTATT
1 ATATTATTATT
909394 ATATTATTATT
1 ATATTATTATT
909405 AT-TATATTATT
1 ATAT-TATTATT
909416 AT
1 AT
909418 TAAATAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 1 0.04
11 22 0.96
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
ATATTATTATT
Found at i:909427 original size:14 final size:13
Alignment explanation
Indices: 909342--909430 Score: 71
Period size: 14 Copynumber: 7.0 Consensus size: 13
909332 TTCATTTTAC
909342 TTAAATTATTATTA
1 TTAAA-TATTATTA
**
909356 TTAAA-ATTAAAA
1 TTAAATATTATTA
* *
909368 TT-ATTGTTATTA
1 TTAAATATTATTA
909380 -TAAATATTATTA
1 TTAAATATTATTA
909392 TT--ATATTATTA
1 TTAAATATTATTA
*
909403 TTATTATATTATTA
1 TTA-AATATTATTA
909417 TTAAATAATTATTA
1 TTAAAT-ATTATTA
909431 CAAACCCAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
11 13 0.22
12 19 0.32
13 3 0.05
14 24 0.41
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (13 bp):
TTAAATATTATTA
Found at i:909430 original size:3 final size:3
Alignment explanation
Indices: 909346--909419 Score: 71
Period size: 3 Copynumber: 25.3 Consensus size: 3
909336 TTTTACTTAA
** ** * * *
909346 ATT ATT ATT ATT AAA ATT AAA ATT ATT GTT ATT ATA AAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
909394 A-T ATT ATT ATT ATT A-T ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
909420 AATAATTATT
Statistics
Matches: 55, Mismatches: 14, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
2 4 0.07
3 51 0.93
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:910144 original size:13 final size:13
Alignment explanation
Indices: 910126--910154 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
910116 ACCACCGTTA
910126 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
910139 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
910152 CGG
1 CGG
910155 AGTACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:910745 original size:19 final size:19
Alignment explanation
Indices: 910707--910744 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
910697 TATAATTTAG
910707 TCATTTATTTTATATGTTT
1 TCATTTATTTTATATGTTT
910726 TCATTTATTTTAT-TGTTT
1 TCATTTATTTTATATGTTT
910744 T
1 T
910745 TAAAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.71
Consensus pattern (19 bp):
TCATTTATTTTATATGTTT
Found at i:910857 original size:13 final size:13
Alignment explanation
Indices: 910839--910877 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
910829 GTAATTAAAT
910839 TTTTAAATATTTA
1 TTTTAAATATTTA
*
910852 TTTTAAATGAATTA
1 TTTTAAAT-ATTTA
910866 TTTT-AATATTTA
1 TTTTAAATATTTA
910878 GCTTTCAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 4 0.17
13 11 0.48
14 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (13 bp):
TTTTAAATATTTA
Found at i:915181 original size:2 final size:2
Alignment explanation
Indices: 915174--915201 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
915164 ATATAAAATA
915174 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
915202 TTGTTTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:922441 original size:9 final size:9
Alignment explanation
Indices: 922420--922463 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
922410 TTCTGACTCC
*
922420 TCGTTGTCA
1 TCGTCGTCA
*
922429 TCGTCGTCG
1 TCGTCGTCA
922438 TCGTCGTCA
1 TCGTCGTCA
* *
922447 CCATCGTCA
1 TCGTCGTCA
922456 TCGTCGTC
1 TCGTCGTC
922464 GTCCTGAGCA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.09, C:0.34, G:0.23, T:0.34
Consensus pattern (9 bp):
TCGTCGTCA
Found at i:922466 original size:21 final size:21
Alignment explanation
Indices: 922427--922466 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
922417 TCCTCGTTGT
*
922427 CATCGTCGTCGTCGTCGTCAC
1 CATCGTCATCGTCGTCGTCAC
922448 CATCGTCATCGTCGTCGTC
1 CATCGTCATCGTCGTCGTC
922467 CTGAGCAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.38, G:0.23, T:0.30
Consensus pattern (21 bp):
CATCGTCATCGTCGTCGTCAC
Found at i:924458 original size:111 final size:111
Alignment explanation
Indices: 924318--924539 Score: 390
Period size: 111 Copynumber: 2.0 Consensus size: 111
924308 ATTACAAAAA
* *
924318 TTAATTCTTAATCTAATAATCGTGCATTAAATAAATCAGCTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* * *
924383 AATTAAAACGTTAAAATATTACTGTATCAGCAAATTGTCGAGATAT
66 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
924429 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
924494 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
924540 ATGATTTCCA
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 105 1.00
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.37
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:924644 original size:17 final size:18
Alignment explanation
Indices: 924603--924641 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
924593 ATTATATTAC
924603 TAAAATA-TTAAATAAAG
1 TAAAATACTTAAATAAAG
*
924620 TAAAATACTTAAATAAAT
1 TAAAATACTTAAATAAAG
924638 TAAA
1 TAAA
924642 TACATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (18 bp):
TAAAATACTTAAATAAAG
Found at i:924702 original size:10 final size:10
Alignment explanation
Indices: 924684--924713 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
924674 TTAAAAAGAA
*
924684 AGAGTATTTG
1 AGAGAATTTG
924694 AGAGAATTTG
1 AGAGAATTTG
924704 AGAGAATTTG
1 AGAGAATTTG
924714 GTGTGATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.30, T:0.33
Consensus pattern (10 bp):
AGAGAATTTG
Found at i:924985 original size:30 final size:29
Alignment explanation
Indices: 924923--924985 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
924913 TACTGCTACG
** *
924923 GGTGTTAGATCGGGAAATATAATTTGACC
1 GGTGTTAGATCGGGAAATATAAGATCACC
* *
924952 GGTGTTAGATCGGTAAATATACCGATCACC
1 GGTGTTAGATCGGGAAATATA-AGATCACC
924982 GGTG
1 GGTG
924986 ATTTTTTGAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (29 bp):
GGTGTTAGATCGGGAAATATAAGATCACC
Found at i:933587 original size:2 final size:2
Alignment explanation
Indices: 933580--933664 Score: 163
Period size: 2 Copynumber: 43.0 Consensus size: 2
933570 ACATATGATA
933580 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
933622 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
933663 AT
1 AT
933665 TGCTACACAA
Statistics
Matches: 82, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 81 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:941590 original size:2 final size:2
Alignment explanation
Indices: 941583--941648 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
941573 TTTAAAAGTC
941583 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
941625 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
941649 ATCCACACAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:942829 original size:22 final size:21
Alignment explanation
Indices: 942788--942830 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
942778 TATTAATATG
*
942788 TTGTTATGGAAATGTTATGTT
1 TTGTTATGGAAATGTAATGTT
942809 TTGTATATGGAAAT-TAAATGTT
1 TTGT-TATGGAAATGT-AATGTT
942831 AGCATATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.49
Consensus pattern (21 bp):
TTGTTATGGAAATGTAATGTT
Found at i:943375 original size:16 final size:16
Alignment explanation
Indices: 943354--943385 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
943344 CAAATATGAG
943354 AAGTTGTTTACAATTA
1 AAGTTGTTTACAATTA
*
943370 AAGTTGTTTAGAATTA
1 AAGTTGTTTACAATTA
943386 GAATTACTTA
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:0.38, C:0.03, G:0.16, T:0.44
Consensus pattern (16 bp):
AAGTTGTTTACAATTA
Found at i:946589 original size:20 final size:20
Alignment explanation
Indices: 946564--946798 Score: 181
Period size: 20 Copynumber: 11.7 Consensus size: 20
946554 GATTTTCCAT
** *
946564 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGTA
**
946584 AATCGCAACGCGAA-CATATA
1 AATCGCAACGCGAATC-CGTA
* * *
946604 AATCGCAATGCGATTCTG-A
1 AATCGCAACGCGAATCCGTA
* * *
946623 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATCCGT-A
*
946645 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
946665 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
946685 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGAATCCGTA
* * *
946705 AATCACAACGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
946725 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
*
946745 AATCGCAACGACAAAAT--GTAA
1 AATCGCAACG-C-GAATCCGT-A
*
946766 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
946786 AATCGCAACGCGA
1 AATCGCAACGCGA
946799 TTTTTAAAGC
Statistics
Matches: 168, Mismatches: 37, Indels: 20
0.75 0.16 0.09
Matches are distributed among these distances:
19 3 0.02
20 130 0.77
21 32 0.19
22 3 0.02
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGTA
Found at i:946611 original size:40 final size:40
Alignment explanation
Indices: 946564--946795 Score: 218
Period size: 40 Copynumber: 5.8 Consensus size: 40
946554 GATTTTCCAT
* ** * * *
946564 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAACATGTA
* * * * *
946604 AATCGCAATGCG-ATTC-TGACTATCGCAACGAGTATC-CGTAA
1 AATCGCAACGCGTATCCGT-A-AATCGCAACGAG-AACATGT-A
* *
946645 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAACATGTA
* * * *
946685 AATCGCAACGCGTATCTGTAAATCACAACGAGAATACGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAACATGTA
* * *
946725 AATCGCAATGCGTATCCGTAAATCGCAACGACAAAATGTAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAACATGT-A
946766 AATCGCAACGCGTATCCGTAAATCGCAACG
1 AATCGCAACGCGTATCCGTAAATCGCAACG
946796 CGATTTTTAA
Statistics
Matches: 161, Mismatches: 23, Indels: 15
0.81 0.12 0.08
Matches are distributed among these distances:
39 3 0.02
40 95 0.59
41 58 0.36
42 4 0.02
43 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGAGAACATGTA
Found at i:946727 original size:121 final size:121
Alignment explanation
Indices: 946564--946795 Score: 297
Period size: 121 Copynumber: 1.9 Consensus size: 121
946554 GATTTTCCAT
* * * * *
946564 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATAAATCGCAATGCG-ATTC-TGACTAT
1 AATCGCAACGCGAATATGAAAATCACAACGAGAACACATAAATCGCAATGCGTATCCGT-A-AAT
** **
946627 CGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
64 CGCAACGACAAAACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
* * * * *
946685 AATCGCAACGCGTATCTGTAAATCACAACGAGAATACGTAAATCGCAATGCGTATCCGTAAATCG
1 AATCGCAACGCGAATATGAAAATCACAACGAGAACACATAAATCGCAATGCGTATCCGTAAATCG
*
946750 CAACGACAAAATGTAAAATCGCAACGCGTATCCGTAAATCGCAACG
66 CAACGACAAAACGTAAAATCGCAACGCGTATCCGTAAATCGCAACG
946796 CGATTTTTAA
Statistics
Matches: 94, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
121 89 0.95
122 4 0.04
123 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (121 bp):
AATCGCAACGCGAATATGAAAATCACAACGAGAACACATAAATCGCAATGCGTATCCGTAAATCG
CAACGACAAAACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
Found at i:947384 original size:20 final size:19
Alignment explanation
Indices: 947359--947430 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
947349 TTCTAAACTT
947359 AAAATCGCAACATGAAAATG
1 AAAATCGCAACA-GAAAATG
*
947379 AAAATCGCAACACAAAAATG
1 AAAATCGCAACA-GAAAATG
** *
947399 ACTATCCCAACGAGAGAAATG
1 AAAATCGCAAC-AGA-AAATG
947420 AAAATCGCAAC
1 AAAATCGCAAC
947431 GAGAGAATCG
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
20 27 0.66
21 14 0.34
ACGTcount: A:0.53, C:0.21, G:0.14, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACAGAAAATG
Found at i:947419 original size:21 final size:21
Alignment explanation
Indices: 947374--947437 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
947364 CGCAACATGA
* * *
947374 AAATGAAAATCGCAAC-ACAA
1 AAATGAAAATCCCAACGAGAG
**
947394 AAATGACTATCCCAACGAGAG
1 AAATGAAAATCCCAACGAGAG
*
947415 AAATGAAAATCGCAACGAGAG
1 AAATGAAAATCCCAACGAGAG
947436 AA
1 AA
947438 TCGCAACGCG
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
20 13 0.37
21 22 0.63
ACGTcount: A:0.53, C:0.19, G:0.17, T:0.11
Consensus pattern (21 bp):
AAATGAAAATCCCAACGAGAG
Found at i:947460 original size:19 final size:19
Alignment explanation
Indices: 947359--947480 Score: 74
Period size: 19 Copynumber: 6.5 Consensus size: 19
947349 TTCTAAACTT
**
947359 AAAATCGCAACATGAAAATG
1 AAAATCGCAACGCG-AAATG
* *
947379 AAAATCGCAACACAAAAATG
1 AAAATCGCAACGC-GAAATG
** * *
947399 ACTATCCCAACGAGAGAAATG
1 AAAATCGCAAC--GCGAAATG
947420 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
*
947434 AGAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
**
947453 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATG
947472 AAAATCGCA
1 AAAATCGCA
947481 TTGCGATTTT
Statistics
Matches: 78, Mismatches: 16, Indels: 17
0.70 0.14 0.15
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 1 0.01
18 1 0.01
19 26 0.33
20 25 0.32
21 12 0.15
ACGTcount: A:0.50, C:0.22, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:947523 original size:33 final size:33
Alignment explanation
Indices: 947481--947602 Score: 136
Period size: 33 Copynumber: 3.5 Consensus size: 33
947471 CAAAATCGCA
947481 TTGCGATTTTCATTTCGCGTTGCAATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCAATTCTCTCG
* *
947514 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCAATTCTCTCG
**
947547 TTGCGATAGTCATTTCCGCGTTGCGATTTTCATTCTCTCG
1 TTGCGATTTTCATTT-CGCGTTGC-A-----ATTCTCTCG
*
947587 TTGTGATTTTCATTTC
1 TTGCGATTTTCATTTC
947603 AACCAAAAGA
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
33 44 0.60
34 7 0.10
39 1 0.01
40 21 0.29
ACGTcount: A:0.12, C:0.23, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCAATTCTCTCG
Found at i:947579 original size:20 final size:21
Alignment explanation
Indices: 947539--947602 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 21
947529 CGCATTGCGA
* **
947539 TTCTCTCGTTGCGATAGTCAT
1 TTCTCGCGTTGCGATTTTCAT
947560 TTC-CGCGTTGCGATTTTCA-
1 TTCTCGCGTTGCGATTTTCAT
* *
947579 TTCTCTCGTTGTGATTTTCAT
1 TTCTCGCGTTGCGATTTTCAT
947600 TTC
1 TTC
947603 AACCAAAAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 3 0.08
20 27 0.75
21 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.17, T:0.48
Consensus pattern (21 bp):
TTCTCGCGTTGCGATTTTCAT
Found at i:949642 original size:21 final size:21
Alignment explanation
Indices: 949618--949687 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
949608 CTATCATTCC
949618 TCAAGAGTCCCCTCCCACCAT
1 TCAAGAGTCCCCTCCCACCAT
* * ** * *
949639 TCAAGAGGCCACTGTCATCGT
1 TCAAGAGTCCCCTCCCACCAT
*
949660 TGAAGAGGT-CCCTCCCACCAT
1 TCAAGA-GTCCCCTCCCACCAT
949681 TCAAGAG
1 TCAAGAG
949688 CCCGATTCAC
Statistics
Matches: 34, Mismatches: 14, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 32 0.94
22 1 0.03
ACGTcount: A:0.26, C:0.36, G:0.19, T:0.20
Consensus pattern (21 bp):
TCAAGAGTCCCCTCCCACCAT
Found at i:949645 original size:42 final size:42
Alignment explanation
Indices: 949569--949687 Score: 116
Period size: 42 Copynumber: 2.8 Consensus size: 42
949559 GACTCGCCTG
* * * * * * *
949569 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCAAGAGTCCCCTCCCACCATTCAAGAGGCCACTA
*
949611 TCATTCCTCAAGAGTCCCCTCCCACCATTCAAGAGGCCACTG
1 TCATTCCTCAAGAGTCCCCTCCCACCATTCAAGAGGCCACTA
* *
949653 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTC-CTCAAGA-GTCCCCTCCCACCATTCAAGAG
949688 CCCGATTCAC
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 2 0.03
42 61 0.94
43 2 0.03
ACGTcount: A:0.24, C:0.36, G:0.17, T:0.23
Consensus pattern (42 bp):
TCATTCCTCAAGAGTCCCCTCCCACCATTCAAGAGGCCACTA
Found at i:951059 original size:14 final size:14
Alignment explanation
Indices: 951040--951075 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
951030 ATTGTTTAAT
951040 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
951054 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
951068 TGATTTGT
1 TGATTTGT
951076 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:951247 original size:14 final size:14
Alignment explanation
Indices: 951230--951256 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
951220 AATGCAAAAT
951230 TAAAATCGCAACGA
1 TAAAATCGCAACGA
951244 TAAAATCGCAACG
1 TAAAATCGCAACG
951257 CGAAACTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.22, G:0.15, T:0.15
Consensus pattern (14 bp):
TAAAATCGCAACGA
Found at i:951251 original size:33 final size:33
Alignment explanation
Indices: 951182--951254 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
951172 AAAAATGACT
* *
951182 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCAAAATGAAAATCGCAACGAGAAA
* * *
951215 ATCGTAATGCAAAATTAAAATCGCAACGATAAA
1 ATCGCAATGCAAAATGAAAATCGCAACGAGAAA
951248 ATCGCAA
1 ATCGCAA
951255 CGCGAAACTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.18, G:0.18, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCAAAATGAAAATCGCAACGAGAAA
Found at i:951289 original size:19 final size:19
Alignment explanation
Indices: 951267--951404 Score: 125
Period size: 19 Copynumber: 7.7 Consensus size: 19
951257 CGAAACTAAA
*
951267 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
951286 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
951302 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
951319 TTCGCATTACGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
951335 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
**
951352 TTCGCATTGCGATAGTCATT
1 TTCGCATTGCGATTTTCA-T
*
951372 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
951391 TTCGCATTGCGATT
1 TTCGCATTGCGATT
951405 CTCTCGTTGC
Statistics
Matches: 93, Mismatches: 15, Indels: 22
0.72 0.12 0.17
Matches are distributed among these distances:
14 11 0.12
16 13 0.14
17 13 0.14
19 40 0.43
20 16 0.17
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:951376 original size:20 final size:19
Alignment explanation
Indices: 951348--951444 Score: 78
Period size: 20 Copynumber: 5.3 Consensus size: 19
951338 GTTGCGATTT
951348 TCATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATAG
* **
951367 TCATTTTCGCGTTGCGATTT
1 TCA-TTTCGCATTGCGATAG
951387 TCATTTCGCATTGCGAT--
1 TCATTTCGCATTGCGATAG
*
951404 TC-TCTCG--TTGCGATAG
1 TCATTTCGCATTGCGATAG
* *
951420 TAATTTCCGCGTTGCGATAG
1 TCATTT-CGCATTGCGATAG
*
951440 ACATT
1 TCATT
951445 AAGATGATTG
Statistics
Matches: 62, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
14 7 0.11
16 5 0.08
17 4 0.06
18 2 0.03
19 16 0.26
20 28 0.45
ACGTcount: A:0.18, C:0.22, G:0.21, T:0.40
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:951404 original size:72 final size:71
Alignment explanation
Indices: 951271--951444 Score: 223
Period size: 72 Copynumber: 2.5 Consensus size: 71
951261 ACTAAATTCG
*
951271 CGTTGCGATTTTCATTTCGCATTGCGAT--TC---CCTCGTTGCGATTTTCATTTCGCATTACGA
1 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTCCGCGTTGCGATTTTCATTTCGCATTACGA
951331 TTCTCT
66 TTCTCT
* *
951337 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTTCGCGTTGCGATTTTCATTTCGCATTGCG
1 CGTTGCGATTTTCATTTCGCATTGCGATAGTCA-TTCCGCGTTGCGATTTTCATTTCGCATTACG
951402 ATTCTCT
65 ATTCTCT
** * * *
951409 CGTTGCGATAGTAATTTCCGCGTTGCGATAGACATT
1 CGTTGCGATTTTCATTT-CGCATTGCGATAGTCATT
951445 AAGATGATTG
Statistics
Matches: 93, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
66 28 0.30
68 2 0.02
72 49 0.53
73 14 0.15
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.42
Consensus pattern (71 bp):
CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTCCGCGTTGCGATTTTCATTTCGCATTACGA
TTCTCT
Found at i:951426 original size:33 final size:33
Alignment explanation
Indices: 951271--951417 Score: 213
Period size: 33 Copynumber: 4.3 Consensus size: 33
951261 ACTAAATTCG
*
951271 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
951304 CGTTGCGATTTTCATTTCGCATTACGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
951337 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTTCG
1 CGTTGCGATTTTCATTTCGCATTGCGAT--TC----TCT
951376 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
951409 CGTTGCGAT
1 CGTTGCGAT
951418 AGTAATTTCC
Statistics
Matches: 103, Mismatches: 5, Indels: 12
0.86 0.04 0.10
Matches are distributed among these distances:
33 69 0.67
35 2 0.02
37 2 0.02
39 30 0.29
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:951483 original size:20 final size:20
Alignment explanation
Indices: 951410--951483 Score: 53
Period size: 20 Copynumber: 3.6 Consensus size: 20
951400 CGATTCTCTC
* *
951410 GTTGCGATAGTAATTTCCGC
1 GTTGCGATAGTCATTTCCGT
* **
951430 GTTGCGATAGACA-TTAAGAT
1 GTTGCGATAGTCATTTCCG-T
*
951450 GATTGC-AAACGTCATTTCCGT
1 G-TTGCGATA-GTCATTTCCGT
951471 GTTGCGATAGTCA
1 GTTGCGATAGTCA
951484 AATGAATGCC
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
19 3 0.08
20 22 0.56
21 11 0.28
22 3 0.08
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCGT
Found at i:953198 original size:16 final size:16
Alignment explanation
Indices: 953177--953209 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
953167 TGACAATAAG
953177 CCGTCAGTTGGGCAAA
1 CCGTCAGTTGGGCAAA
953193 CCGTCAGTTGGGCAAA
1 CCGTCAGTTGGGCAAA
953209 C
1 C
953210 GATGCTTCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.30, T:0.18
Consensus pattern (16 bp):
CCGTCAGTTGGGCAAA
Found at i:954006 original size:24 final size:24
Alignment explanation
Indices: 953972--954025 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
953962 CTGAAAAATC
953972 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
* *
953996 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
954020 ATCAAA
1 ATCAAA
954026 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.24
Consensus pattern (24 bp):
ATCAAAATCTGAGTATTGACCAAG
Found at i:955109 original size:20 final size:20
Alignment explanation
Indices: 954885--955175 Score: 268
Period size: 20 Copynumber: 14.5 Consensus size: 20
954875 GTCAGAATCT
954885 CGTTGCGATTTACAG-ATTCG
1 CGTTGCGATTTAC-GTATTCG
*
954905 CATTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTATTCG
*
954925 CATTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTATTCG
*
954945 CATTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTATTCG
* * *
954965 CATTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCG
* *
954985 CATTGCGATTTACGTATTCT
1 CGTTGCGATTTACGTATTCG
*
955005 CGTTGCGATTTACAG-ATACG
1 CGTTGCGATTTAC-GTATTCG
*
955025 CGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGTATTCG
* * *
955045 CGTTGCGATTTATGGATACG
1 CGTTGCGATTTACGTATTCG
955065 CGTTGCGATTTTACGTATT-G
1 CGTTGCGA-TTTACGTATTCG
* *
955085 TCGTTGCGATTTACGGATACG
1 -CGTTGCGATTTACGTATTCG
* * *
955106 CGTTGTGATAGT-CAG-AATCG
1 CGTTGCGAT-TTAC-GTATTCG
** *
955126 CGTTGCGATTTATATGTTCG
1 CGTTGCGATTTACGTATTCG
* * * *
955146 CGTTGTGATTTTCATATTCA
1 CGTTGCGATTTACGTATTCG
955166 CGTTGCGATT
1 CGTTGCGATT
955176 ATGGAAAATC
Statistics
Matches: 225, Mismatches: 36, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
19 3 0.01
20 203 0.90
21 19 0.08
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTACGTATTCG
Found at i:955274 original size:20 final size:19
Alignment explanation
Indices: 955225--955278 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
955215 ATTCTTCATA
955225 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
955244 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
955265 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
955279 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:955412 original size:2 final size:2
Alignment explanation
Indices: 955407--955435 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
955397 TAAAAAATTA
955407 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
955436 AGTCGGGTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:955833 original size:31 final size:31
Alignment explanation
Indices: 955790--955853 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
955780 TGACCACACC
* * *
955790 TAATTAATTAAAAATGAAAGTGACTATATCT
1 TAATTAAATAAAAACGAAAGTGACCATATCT
955821 TAATTAAATAAAAACGAAAGTGACCATATCT
1 TAATTAAATAAAAACGAAAGTGACCATATCT
955852 TA
1 TA
955854 TGTTTTTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.31
Consensus pattern (31 bp):
TAATTAAATAAAAACGAAAGTGACCATATCT
Found at i:956042 original size:17 final size:19
Alignment explanation
Indices: 956001--956043 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
955991 GGATATAATC
*
956001 TTTAATATATTTTATCTTT
1 TTTAATATATTTTATCTTA
*
956020 TTTAATTTA-TTTA-CTTA
1 TTTAATATATTTTATCTTA
956037 TTTAATA
1 TTTAATA
956044 ATCAAACTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 9 0.43
18 4 0.19
19 8 0.38
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTAATATATTTTATCTTA
Found at i:958465 original size:19 final size:19
Alignment explanation
Indices: 958441--958481 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
958431 CTATGCCAGC
958441 ATCTACATAGCCTGTCAGT
1 ATCTACATAGCCTGTCAGT
*
958460 ATCTACATAGTCTGTCAGT
1 ATCTACATAGCCTGTCAGT
958479 ATC
1 ATC
958482 GTATCTCCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (19 bp):
ATCTACATAGCCTGTCAGT
Found at i:963272 original size:18 final size:18
Alignment explanation
Indices: 963249--963286 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
963239 TATTAATTTT
963249 TTTAA-TAATTTCGGTTAA
1 TTTAATTAATTT-GGTTAA
963267 TTTAATTAATTTGGTTAA
1 TTTAATTAATTTGGTTAA
963285 TT
1 TT
963287 GGCCGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.32, C:0.03, G:0.11, T:0.55
Consensus pattern (18 bp):
TTTAATTAATTTGGTTAA
Found at i:973766 original size:2 final size:2
Alignment explanation
Indices: 973761--973821 Score: 61
Period size: 2 Copynumber: 31.0 Consensus size: 2
973751 ATAGATATAT
* * * * *
973761 AG AG AG AA AT AG AG AT AG AG AG AG AG AG AG AG GG AG AG AG GG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
973803 AG AG AG GG AG AG -G AG AG AG
1 AG AG AG AG AG AG AG AG AG AG
973822 GAGGGGGAGG
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.46, C:0.00, G:0.51, T:0.03
Consensus pattern (2 bp):
AG
Found at i:973772 original size:18 final size:18
Alignment explanation
Indices: 973751--973785 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
973741 ATATATAGAT
* *
973751 ATAGATATATAGAGAGAA
1 ATAGAGATAGAGAGAGAA
973769 ATAGAGATAGAGAGAGA
1 ATAGAGATAGAGAGAGA
973786 GAGAGAGGGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.29, T:0.17
Consensus pattern (18 bp):
ATAGAGATAGAGAGAGAA
Found at i:973825 original size:16 final size:17
Alignment explanation
Indices: 973777--973831 Score: 69
Period size: 16 Copynumber: 3.3 Consensus size: 17
973767 AAATAGAGAT
973777 AGAGAGAGAGAGAGAGGG
1 AGAG-GAGAGAGAGAGGG
*
973795 AGA-GAGGGAGAGAGGG
1 AGAGGAGAGAGAGAGGG
973811 AGAGGAGAGAG-GAGGG
1 AGAGGAGAGAGAGAGGG
*
973827 GGAGG
1 AGAGG
973832 GCGGGGAGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 24 0.73
17 6 0.18
18 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (17 bp):
AGAGGAGAGAGAGAGGG
Found at i:973831 original size:22 final size:21
Alignment explanation
Indices: 973782--973849 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 21
973772 GAGATAGAGA
*
973782 GAGAGAGAGAG-GGAGAGAGG
1 GAGAGAGGGAGAGGAGAGAGG
973802 GAGAGAGGGAGAGGAGAGAGG
1 GAGAGAGGGAGAGGAGAGAGG
* * * * *
973823 AGGGGGAGGGCGGGGAGAGAGA
1 -GAGAGAGGGAGAGGAGAGAGG
973845 GAGAG
1 GAGAG
973850 TCACGTTAAC
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
20 10 0.26
21 12 0.32
22 16 0.42
ACGTcount: A:0.35, C:0.01, G:0.63, T:0.00
Consensus pattern (21 bp):
GAGAGAGGGAGAGGAGAGAGG
Done.