Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold72
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: 5928628
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 261288 characters in sequence are not A, C, G, or T
File 7 of 39
Found at i:838507 original size:79 final size:79
Alignment explanation
Indices: 838415--838711 Score: 298
Period size: 79 Copynumber: 3.8 Consensus size: 79
838405 CTGAGTCCTC
* ** * * * *
838415 TAGAGCATC-TTGGTGTTTTTATATCAAAACATATATATTAATGTCATTTTAGGGAATTTTATGA
1 TAGAGCA-CGTTGGTATTTTTATATCAAAACATATGCATTAAGGTCATTTTAGGAAATTTCATAA
*
838479 GAAATTCAAGT-CTT
65 GAAATCCAAGTACTT
* *
838493 TAGAAGCACGTTGGTATTTTTATATCAAAACATGTGCATTAAGGTTATTTTAGGAAATTTCATAA
1 TAG-AGCACGTTGGTATTTTTATATCAAAACATATGCATTAAGGTCATTTTAGGAAATTTCATAA
838558 GAAATCCAAGTAC-T
65 GAAATCCAAGTACTT
* * * * *
838572 TAGGAGCATGTTGGTATTTTTATCTCGATACATCTGCATTAAGGTCATTTTAGGAAATTTCATAA
1 TA-GAGCACGTTGGTATTTTTATATCAAAACATATGCATTAAGGTCATTTTAGGAAATTTCATAA
838637 GAAATCCAAGTAC-T
65 GAAATCCAAGTACTT
*** * ** * * * *
838651 TAGGAGTGTGTTGGTATTTTCATATTGATACATGTGCATTAAAGTCATTTTA-GAAGTTTCA
1 TA-GAGCACGTTGGTATTTTTATATCAAAACATATGCATTAAGGTCATTTTAGGAAATTTCA
838712 CGCTAAAACC
Statistics
Matches: 191, Mismatches: 24, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
78 12 0.06
79 177 0.93
80 2 0.01
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.39
Consensus pattern (79 bp):
TAGAGCACGTTGGTATTTTTATATCAAAACATATGCATTAAGGTCATTTTAGGAAATTTCATAAG
AAATCCAAGTACTT
Found at i:839208 original size:21 final size:20
Alignment explanation
Indices: 839176--839220 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
839166 GAACTTGTCA
*
839176 AAAAGAGCAAAAAAT-TCATT
1 AAAAGAACAAAAAATCTC-TT
839196 AAAAGAACAAAAAAATCTCTT
1 AAAAGAAC-AAAAAATCTCTT
839217 AAAA
1 AAAA
839221 CGCCCTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
21 13 0.59
22 2 0.09
ACGTcount: A:0.64, C:0.11, G:0.07, T:0.18
Consensus pattern (20 bp):
AAAAGAACAAAAAATCTCTT
Found at i:839621 original size:23 final size:23
Alignment explanation
Indices: 839587--839638 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
839577 TTTTTCCTTA
839587 ATTTTTTATTTTTA-G-TTCTTGT
1 ATTTTTTATTTTTATGTTTC-TGT
839609 ATTTTTTATTTTTATGTTTCTGT
1 ATTTTTTATTTTTATGTTTCTGT
839632 ATTTTTT
1 ATTTTTT
839639 TGAAATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.50
23 11 0.39
24 3 0.11
ACGTcount: A:0.13, C:0.04, G:0.08, T:0.75
Consensus pattern (23 bp):
ATTTTTTATTTTTATGTTTCTGT
Found at i:841786 original size:39 final size:40
Alignment explanation
Indices: 841733--841820 Score: 115
Period size: 39 Copynumber: 2.2 Consensus size: 40
841723 CTAAAATATT
* *
841733 ATATTAATATTAAATACTTAAAATATACTATTTATTATTAAA
1 ATATT-ATA-TAAATACTTAAAATATACAAATTATTATTAAA
* *
841775 A-ATTATATAAATATTTAAAATATTCAAATTATTATTAAA
1 ATATTATATAAATACTTAAAATATACAAATTATTATTAAA
841814 ATATTAT
1 ATATTAT
841821 TTATATTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
39 29 0.71
40 8 0.20
41 3 0.07
42 1 0.02
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.45
Consensus pattern (40 bp):
ATATTATATAAATACTTAAAATATACAAATTATTATTAAA
Found at i:841829 original size:17 final size:18
Alignment explanation
Indices: 841750--841854 Score: 85
Period size: 20 Copynumber: 5.8 Consensus size: 18
841740 TATTAAATAC
841750 TTAAAATATACTATTTATTA
1 TTAAAATAT--TATTTATTA
* *
841770 TTAAAA-ATTATATAAATA
1 TTAAAATATTAT-TTATTA
*
841788 TTTAAAATATTCAAATTATTA
1 -TTAAAATATT--ATTTATTA
841809 TTAAAATATTATTTA-TA
1 TTAAAATATTATTTATTA
*
841826 TT--AATA-TAATTATTA
1 TTAAAATATTATTTATTA
841841 TTAAAATATTATTT
1 TTAAAATATTATTT
841855 TACAATTTTC
Statistics
Matches: 68, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
14 5 0.07
15 8 0.12
17 11 0.16
18 12 0.18
19 8 0.12
20 19 0.28
21 4 0.06
22 1 0.01
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAAAATATTATTTATTA
Found at i:841946 original size:21 final size:21
Alignment explanation
Indices: 841904--841952 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
841894 TACTAAAAAC
* *
841904 TATTT-ATCATTAAATTATTAA
1 TATTTAAT-ATTAAAATAGTAA
*
841925 TTTTTAATATTAAAATAGTAA
1 TATTTAATATTAAAATAGTAA
841946 TATTTAA
1 TATTTAA
841953 AAAATAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
TATTTAATATTAAAATAGTAA
Found at i:841964 original size:14 final size:15
Alignment explanation
Indices: 841929--842006 Score: 54
Period size: 14 Copynumber: 5.1 Consensus size: 15
841919 TATTAATTTT
*
841929 TAATA-TTAAAATAG
1 TAATATTTAAAATAA
841943 TAATATTTAAAA-AA
1 TAATATTTAAAATAA
*
841957 TAATATTTAAGACTAA
1 TAATATTTAA-AATAA
* *
841973 -AATATTATATTAATAT
1 TAATATT-TA-AAATAA
*
841989 TAAATACTTAAAATAA
1 T-AATATTTAAAATAA
842005 TA
1 TA
842007 TTGTTTATTA
Statistics
Matches: 49, Mismatches: 8, Indels: 13
0.70 0.11 0.19
Matches are distributed among these distances:
14 16 0.33
15 14 0.29
16 12 0.24
17 2 0.04
18 5 0.10
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (15 bp):
TAATATTTAAAATAA
Found at i:842428 original size:19 final size:19
Alignment explanation
Indices: 842404--842468 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 19
842394 TAGCCAAACT
842404 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAATA
842423 TGTATCGAT--AC---A-A
1 TGTATCGATACACAAAATA
842436 TGTATCGATACACAAAAAATA
1 TGTATCGATACAC--AAAATA
842457 TGTATCGATACA
1 TGTATCGATACA
842469 TTGGCTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
19 9 0.24
20 1 0.03
21 13 0.34
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (19 bp):
TGTATCGATACACAAAATA
Found at i:842440 original size:13 final size:13
Alignment explanation
Indices: 842422--842447 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
842412 TACACAAAAT
842422 ATGTATCGATACA
1 ATGTATCGATACA
842435 ATGTATCGATACA
1 ATGTATCGATACA
842448 CAAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:842445 original size:32 final size:33
Alignment explanation
Indices: 842404--842468 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 33
842394 TAGCCAAACT
842404 TGTATCGATACAC-AAAATATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
842436 TGTATCGATACACAAAAAATATGTATCGATACA
1 TGTATCGATACAC-AAAAATATGTATCGATACA
842469 TTGGCTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.42
34 18 0.58
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:843480 original size:16 final size:17
Alignment explanation
Indices: 843459--843490 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
843449 AATAATTTTA
843459 TTTTATT-AAATAATAT
1 TTTTATTCAAATAATAT
843475 TTTTATTCAAATAATA
1 TTTTATTCAAATAATA
843491 AATTATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTTATTCAAATAATAT
Found at i:843658 original size:3 final size:3
Alignment explanation
Indices: 843650--843681 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
843640 TTACATATTT
*
843650 TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
843682 GGCTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:848044 original size:16 final size:17
Alignment explanation
Indices: 848018--848060 Score: 70
Period size: 17 Copynumber: 2.5 Consensus size: 17
848008 GTATTTAAAG
848018 TAAATAAAAT-AAAATTA
1 TAAA-AAAATAAAAATTA
848035 TAAAAAAATAAAAATTA
1 TAAAAAAATAAAAATTA
848052 TAAAAAAAT
1 TAAAAAAAT
848061 TTAGTTTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAAAAATAAAAATTA
Found at i:849138 original size:2 final size:2
Alignment explanation
Indices: 849131--849164 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
849121 CTAAAAGGAT
849131 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
849165 AAATATAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:851508 original size:1 final size:1
Alignment explanation
Indices: 851502--851561 Score: 57
Period size: 1 Copynumber: 60.0 Consensus size: 1
851492 AAATCTTCAC
* * ** * * *
851502 TTTTTTTTTTTGTTTTTTTTTTTCTTTTTCCTTTTTTTTTTGTTTTGTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
851562 CCAATTGCCA
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.00, C:0.07, G:0.05, T:0.88
Consensus pattern (1 bp):
T
Found at i:851539 original size:31 final size:31
Alignment explanation
Indices: 851503--851563 Score: 115
Period size: 30 Copynumber: 2.0 Consensus size: 31
851493 AATCTTCACT
851503 TTTTTTTTTTGTTTT-TTTTTTTCTTTTTCC
1 TTTTTTTTTTGTTTTGTTTTTTTCTTTTTCC
851533 TTTTTTTTTTGTTTTGTTTTTTTCTTTTTCC
1 TTTTTTTTTTGTTTTGTTTTTTTCTTTTTCC
851564 AATTGCCATG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (31 bp):
TTTTTTTTTTGTTTTGTTTTTTTCTTTTTCC
Found at i:860265 original size:26 final size:26
Alignment explanation
Indices: 860218--860285 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
860208 TTCGTCCTAA
* * **
860218 TTTAAAATTTAAAAATCAGATAATGTT
1 TTTAAAA-TTCAAAATAAGATAACCTT
860245 TTTAAAATTCAAAATAAGATAACCTT
1 TTTAAAATTCAAAATAAGATAACCTT
860271 TTTAAAATTCAAAAT
1 TTTAAAATTCAAAAT
860286 TATCTTATCA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 30 0.81
27 7 0.19
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.38
Consensus pattern (26 bp):
TTTAAAATTCAAAATAAGATAACCTT
Found at i:868104 original size:199 final size:199
Alignment explanation
Indices: 867764--868163 Score: 800
Period size: 199 Copynumber: 2.0 Consensus size: 199
867754 AATCAAGCCT
867764 TTATCGAAACACAACCCCACACAACAAACTGCTACCTTCTAGAACAATAATCTAAATTTTCACAC
1 TTATCGAAACACAACCCCACACAACAAACTGCTACCTTCTAGAACAATAATCTAAATTTTCACAC
867829 AAAATGAACTTTCAAGACAACATGCAAAGTACTAAAATTTCAAAGCTCAGCTCCTATTTAAAGTT
66 AAAATGAACTTTCAAGACAACATGCAAAGTACTAAAATTTCAAAGCTCAGCTCCTATTTAAAGTT
867894 GTTGAAGTACTATGATAAAATTTGCTTTTTACTACCGGACTTGTTCATAACTGTGTATTTTAACT
131 GTTGAAGTACTATGATAAAATTTGCTTTTTACTACCGGACTTGTTCATAACTGTGTATTTTAACT
867959 CACA
196 CACA
867963 TTATCGAAACACAACCCCACACAACAAACTGCTACCTTCTAGAACAATAATCTAAATTTTCACAC
1 TTATCGAAACACAACCCCACACAACAAACTGCTACCTTCTAGAACAATAATCTAAATTTTCACAC
868028 AAAATGAACTTTCAAGACAACATGCAAAGTACTAAAATTTCAAAGCTCAGCTCCTATTTAAAGTT
66 AAAATGAACTTTCAAGACAACATGCAAAGTACTAAAATTTCAAAGCTCAGCTCCTATTTAAAGTT
868093 GTTGAAGTACTATGATAAAATTTGCTTTTTACTACCGGACTTGTTCATAACTGTGTATTTTAACT
131 GTTGAAGTACTATGATAAAATTTGCTTTTTACTACCGGACTTGTTCATAACTGTGTATTTTAACT
868158 CACA
196 CACA
868162 TT
1 TT
868164 CATGGTTTCT
Statistics
Matches: 201, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
199 201 1.00
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (199 bp):
TTATCGAAACACAACCCCACACAACAAACTGCTACCTTCTAGAACAATAATCTAAATTTTCACAC
AAAATGAACTTTCAAGACAACATGCAAAGTACTAAAATTTCAAAGCTCAGCTCCTATTTAAAGTT
GTTGAAGTACTATGATAAAATTTGCTTTTTACTACCGGACTTGTTCATAACTGTGTATTTTAACT
CACA
Found at i:870732 original size:21 final size:21
Alignment explanation
Indices: 870686--870733 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
870676 GGAATATATT
870686 GATACATTATATCAAGGTATC
1 GATACATTATATCAAGGTATC
* *
870707 AATACATTATAT-AATTGTATC
1 GATACATTATATCAA-GGTATC
870728 GATACA
1 GATACA
870734 GGGTCATAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.35
Consensus pattern (21 bp):
GATACATTATATCAAGGTATC
Found at i:870806 original size:20 final size:21
Alignment explanation
Indices: 870777--870823 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
870767 CCCTTGGTGT
* *
870777 CAATATATTACCT-AATGTAG
1 CAATACATTAACTCAATGTAG
*
870797 CAATACATTAAGTCAATGTAG
1 CAATACATTAACTCAATGTAG
870818 CAATAC
1 CAATAC
870824 TTCAAAGCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.30
Consensus pattern (21 bp):
CAATACATTAACTCAATGTAG
Found at i:874009 original size:13 final size:13
Alignment explanation
Indices: 873991--874017 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
873981 ACACTATGCT
873991 TTGTATCGATACA
1 TTGTATCGATACA
874004 TTGTATCGATACA
1 TTGTATCGATACA
874017 T
1 T
874018 GTTCACTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:874049 original size:20 final size:19
Alignment explanation
Indices: 874001--874057 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
873991 TTGTATCGAT
*
874001 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
* *
874020 TCACTGTATCGATACATGG
1 ACATTGTATCGATACATGG
874039 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
874058 AAACTGGCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:874146 original size:33 final size:33
Alignment explanation
Indices: 874086--874154 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
874076 CTACCACTGT
* * *
874086 TTGTATCGATACATGGTACATTATATCGATACA
1 TTGTATCGAAACATGATACATTATATCGATAAA
*
874119 TTGTATCGAAACATGATGA-ATTGTATCGATAAA
1 TTGTATCGAAACATGAT-ACATTATATCGATAAA
874152 TTG
1 TTG
874155 CTTGTAACGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (33 bp):
TTGTATCGAAACATGATACATTATATCGATAAA
Found at i:875913 original size:182 final size:182
Alignment explanation
Indices: 875606--875972 Score: 682
Period size: 182 Copynumber: 2.0 Consensus size: 182
875596 TTAAAGAATC
875606 CAAGGATCCCAACACATTATCCTTAGATGAGCTCATAGGTTCTTTATTAACCTACGAGATGAAGA
1 CAAGGATCCCAACACATTATCCTTAGATGAGCTCATAGGTTCTTTATTAACCTACGAGATGAAGA
875671 TCAAGCATGCACAGGTGCAAGAACCACCGAAGAAAGCAAGTGTCGCCTTCAAGTTAACCATCAAT
66 TCAAGCATGCACAGGTGCAAGAACCACCGAAGAAAGCAAGTGTCGCCTTCAAGTTAACCATCAAT
*
875736 AAAGATGAAA-ATGATAATGATGATGATAACGGTGACTCGAATGAAGAAATAG
131 AAAGAT-AAAGATGATAATGATGATGATAACGGTGACTCAAATGAAGAAATAG
875788 CAAGGATCCCAACACATTATCCTTAGATGAGCTCATAGGTTCTTTATTAACCTACGAGATGAAGA
1 CAAGGATCCCAACACATTATCCTTAGATGAGCTCATAGGTTCTTTATTAACCTACGAGATGAAGA
*
875853 TCAAGCATGCACATGTGCAAGAACCACCGAAGAAAGCAAGTGTCGCCTTCAAGTTAACCATCAAT
66 TCAAGCATGCACAGGTGCAAGAACCACCGAAGAAAGCAAGTGTCGCCTTCAAGTTAACCATCAAT
* *
875918 GAAGATAAAGATGATAATGATGATGATGACGGTGACTCAAATGAAGAAATAG
131 AAAGATAAAGATGATAATGATGATGATAACGGTGACTCAAATGAAGAAATAG
875970 CAA
1 CAA
875973 TGATGGCCAG
Statistics
Matches: 180, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
181 3 0.02
182 177 0.98
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (182 bp):
CAAGGATCCCAACACATTATCCTTAGATGAGCTCATAGGTTCTTTATTAACCTACGAGATGAAGA
TCAAGCATGCACAGGTGCAAGAACCACCGAAGAAAGCAAGTGTCGCCTTCAAGTTAACCATCAAT
AAAGATAAAGATGATAATGATGATGATAACGGTGACTCAAATGAAGAAATAG
Found at i:880350 original size:18 final size:18
Alignment explanation
Indices: 880327--880361 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
880317 TGGATGAATT
*
880327 TGTTATTTAATTATGTTA
1 TGTTATTGAATTATGTTA
*
880345 TGTTATTGAATTTTGTT
1 TGTTATTGAATTATGTT
880362 GATTGATGTG
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:0.23, C:0.00, G:0.14, T:0.63
Consensus pattern (18 bp):
TGTTATTGAATTATGTTA
Found at i:880521 original size:13 final size:13
Alignment explanation
Indices: 880503--880527 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
880493 AACATTCCCC
880503 GTATCGATACATT
1 GTATCGATACATT
880516 GTATCGATACAT
1 GTATCGATACAT
880528 AGGTAATTAT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:883061 original size:13 final size:13
Alignment explanation
Indices: 883043--883067 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
883033 CATTATGCTT
883043 TGTATCGATACAA
1 TGTATCGATACAA
883056 TGTATCGATACA
1 TGTATCGATACA
883068 TGTTCATTAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:883107 original size:20 final size:20
Alignment explanation
Indices: 883052--883108 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 20
883042 TTGTATCGAT
*
883052 ACAA-TGTATCGATACATGT
1 ACAATTGTATCGATACATGG
* * **
883071 TC-ATTATATTAATACATGG
1 ACAATTGTATCGATACATGG
883090 ACAATTGTATCGATACATG
1 ACAATTGTATCGATACATG
883109 AAACTGGCAG
Statistics
Matches: 27, Mismatches: 9, Indels: 3
0.69 0.23 0.08
Matches are distributed among these distances:
18 1 0.04
19 13 0.48
20 13 0.48
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (20 bp):
ACAATTGTATCGATACATGG
Found at i:893831 original size:20 final size:20
Alignment explanation
Indices: 893806--893857 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
893796 GTCAAAAAAT
**
893806 TGTATCGATACATAAGTAAA
1 TGTATCGATACATAACCAAA
**
893826 TGTATCGATACATTTCCAAA
1 TGTATCGATACATAACCAAA
893846 TGTATCGATACA
1 TGTATCGATACA
893858 ATTTGCTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATAACCAAA
Found at i:894861 original size:19 final size:21
Alignment explanation
Indices: 894823--894862 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
894813 AGCCCATATT
*
894823 CATGCATTTTGAGCCATGTCC
1 CATGCATTTTGAGACATGTCC
894844 CATGCATTTT-A-ACATGTCC
1 CATGCATTTTGAGACATGTCC
894863 AACATCTCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 1 0.06
21 10 0.56
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.35
Consensus pattern (21 bp):
CATGCATTTTGAGACATGTCC
Found at i:897679 original size:48 final size:48
Alignment explanation
Indices: 897625--897717 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
897615 CAAAAATCTA
*
897625 CAAAATCAAGAAAACTCCTAAGTAAAAACTCTTAGCACTAAAAGTTTG
1 CAAAATCAAGAAAACCCCTAAGTAAAAACTCTTAGCACTAAAAGTTTG
* * **
897673 CAAAATCTAGAAAACCCCTAGGTAAGGACTCTTAGCACTAAAAGT
1 CAAAATCAAGAAAACCCCTAAGTAAAAACTCTTAGCACTAAAAGT
897718 CTACATATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.45, C:0.20, G:0.13, T:0.22
Consensus pattern (48 bp):
CAAAATCAAGAAAACCCCTAAGTAAAAACTCTTAGCACTAAAAGTTTG
Found at i:897996 original size:65 final size:65
Alignment explanation
Indices: 897879--898100 Score: 225
Period size: 65 Copynumber: 3.4 Consensus size: 65
897869 AGTTAACTTG
** **
897879 AACCTATTTTCTTAGAAATAGTTCAAGCTTAGGAACAAACTCTAAATTTTTTTCTTTTTAAGTCA
1 AACCTATTTTCCAAGAAATAGTTCAAGCTTAGGAATGAACTCTAAATTTTTTTCTTTTTAAGTCA
* * * * *
897944 AACCCATTTTCCAAGAAATAGTTCGAGCTTAGGAATGAACTTTAGATCTTTTTC-TTTTACAGTC
1 AACCTATTTTCCAAGAAATAGTTCAAGCTTAGGAATGAACTCTAAATTTTTTTCTTTTTA-AGTC
898008 A
65 A
* * * * * * *
898009 AACTTATTTT-TACA-AAATAGGTCAAGCCTAAGAATGAACTCTACATTTTTTTTCTTTTTAATT
1 AACCTATTTTCCA-AGAAATAGTTCAAGCTTAGGAATGAACTCTA-AATTTTTTTCTTTTTAAGT
898072 CA
64 CA
* * *
898074 AACCTATGTTCCTAGAAATAGCTCAAG
1 AACCTATTTTCCAAGAAATAGTTCAAG
898101 ACTCTAGGTT
Statistics
Matches: 125, Mismatches: 26, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
64 30 0.24
65 79 0.63
66 16 0.13
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (65 bp):
AACCTATTTTCCAAGAAATAGTTCAAGCTTAGGAATGAACTCTAAATTTTTTTCTTTTTAAGTCA
Found at i:898816 original size:21 final size:21
Alignment explanation
Indices: 898758--898817 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
898748 ATCGGTACAT
* *
898758 TGCTTATTGTATCGATATATTA
1 TGCTAATT-TATCGATACATTA
* * * *
898780 AGCCAATGTATAGATACATTA
1 TGCTAATTTATCGATACATTA
898801 TGCTAATTTATCGATAC
1 TGCTAATTTATCGATAC
898818 TTCAGCATAA
Statistics
Matches: 28, Mismatches: 10, Indels: 1
0.72 0.26 0.03
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (21 bp):
TGCTAATTTATCGATACATTA
Found at i:902290 original size:52 final size:52
Alignment explanation
Indices: 902212--902310 Score: 162
Period size: 52 Copynumber: 1.9 Consensus size: 52
902202 ACATTCTTAA
* *
902212 ATAATAATTATGAATTAAACTATAATTTAGAGAGACTTGTCCTTCTCCCAAT
1 ATAATAACTACGAATTAAACTATAATTTAGAGAGACTTGTCCTTCTCCCAAT
* *
902264 ATAATAACTACGAATTAAACTATAATTTATAGAGATTTGTCCTTCTC
1 ATAATAACTACGAATTAAACTATAATTTAGAGAGACTTGTCCTTCTC
902311 TAAATAAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.37
Consensus pattern (52 bp):
ATAATAACTACGAATTAAACTATAATTTAGAGAGACTTGTCCTTCTCCCAAT
Found at i:902821 original size:20 final size:20
Alignment explanation
Indices: 902783--902821 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
902773 TATTTTTATT
*
902783 TATTATAATTATATTTAAAA
1 TATTATAATTATATATAAAA
902803 TATTATATATT-TATATAAA
1 TATTATA-ATTATATATAAA
902822 TTTTAACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTATAATTATATATAAAA
Found at i:902874 original size:25 final size:26
Alignment explanation
Indices: 902846--902902 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
902836 ATAATTTTTA
902846 TTTTTATTA-TTCATATTTAAATTAT
1 TTTTTATTATTTCATATTTAAATTAT
* *
902871 TTTTTATTATTTTATATTTTAATTAT
1 TTTTTATTATTTCATATTTAAATTAT
902897 TTTTTA
1 TTTTTA
902903 ACATTATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 9 0.31
26 20 0.69
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (26 bp):
TTTTTATTATTTCATATTTAAATTAT
Found at i:902912 original size:26 final size:26
Alignment explanation
Indices: 902858--902912 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
902848 TTTATTATTC
** *
902858 ATATTTAAATTATTTTTTATTATTTT
1 ATATTTAAATTATTTTTTAACATTAT
*
902884 ATATTTTAATTATTTTTTAACATTAT
1 ATATTTAAATTATTTTTTAACATTAT
902910 ATA
1 ATA
902913 ATAATATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (26 bp):
ATATTTAAATTATTTTTTAACATTAT
Found at i:903744 original size:2 final size:2
Alignment explanation
Indices: 903737--903766 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
903727 AAATTAGGTA
*
903737 CT CT CT CT CT CT CT TT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
903767 TTAATGAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:903943 original size:2 final size:2
Alignment explanation
Indices: 903936--903984 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
903926 CCAGCAGCTT
903936 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
903978 TA TA TA T
1 TA TA TA T
903985 TGTAAATAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:905496 original size:25 final size:25
Alignment explanation
Indices: 905459--905509 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
905449 CAAATTTTAC
905459 TTAAAATTAATTTATTTAAATAATT
1 TTAAAATTAATTTATTTAAATAATT
* *
905484 TTAAAA-TATATTTTTTTATATAATT
1 TTAAAATTA-ATTTATTTAAATAATT
905509 T
1 T
905510 GACACATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 2 0.09
25 21 0.91
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TTAAAATTAATTTATTTAAATAATT
Found at i:905719 original size:5 final size:5
Alignment explanation
Indices: 905709--905787 Score: 71
Period size: 5 Copynumber: 16.4 Consensus size: 5
905699 AATAATTTTA
* *
905709 AATAT AATAT AAT-T -ATAT GATATT AATAT AATA- AA-AT AATTAA AATAT
1 AATAT AATAT AATAT AATAT AATA-T AATAT AATAT AATAT AA-TAT AATAT
905757 AATAT AA-AT AA-AT AATAT AAATAT AATAT AA
1 AATAT AATAT AATAT AATAT -AATAT AATAT AA
905788 ATATGTGAAT
Statistics
Matches: 63, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
3 3 0.05
4 14 0.22
5 34 0.54
6 12 0.19
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:905736 original size:24 final size:22
Alignment explanation
Indices: 905695--905790 Score: 94
Period size: 24 Copynumber: 4.4 Consensus size: 22
905685 CCTACTTTAG
*
905695 ATAT-AATAAT-TTTAAATATA
1 ATATAAATAATATATAAATATA
* *
905715 ATATAATTATATGATATTAATATA
1 ATATAAATA-AT-ATATAAATATA
905739 ATA-AAATAAT-TA-AAATATA
1 ATATAAATAATATATAAATATA
905758 ATATAAATAAATAATATAAATATA
1 ATATAAAT-AAT-ATATAAATATA
905782 ATATAAATA
1 ATATAAATA
905791 TGTGAATATA
Statistics
Matches: 62, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
19 9 0.15
20 10 0.16
21 6 0.10
22 4 0.06
23 7 0.11
24 26 0.42
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (22 bp):
ATATAAATAATATATAAATATA
Found at i:905759 original size:43 final size:45
Alignment explanation
Indices: 905695--905790 Score: 126
Period size: 43 Copynumber: 2.2 Consensus size: 45
905685 CCTACTTTAG
* * * * *
905695 ATAT-AATAATTTTAAATATAATATAATTATATGATATTAATATA
1 ATATAAATAATTTAAAATATAATATAAATAAATAATATAAATATA
905739 ATA-AAATAA-TTAAAATATAATATAAATAAATAATATAAATATA
1 ATATAAATAATTTAAAATATAATATAAATAAATAATATAAATATA
905782 ATATAAATA
1 ATATAAATA
905791 TGTGAATATA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
43 32 0.71
44 13 0.29
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (45 bp):
ATATAAATAATTTAAAATATAATATAAATAAATAATATAAATATA
Found at i:905765 original size:11 final size:11
Alignment explanation
Indices: 905707--905791 Score: 86
Period size: 11 Copynumber: 7.6 Consensus size: 11
905697 ATAATAATTT
905707 TAAATATAATA
1 TAAATATAATA
*
905718 TAATTATATGATA
1 TAA--ATATAATA
*
905731 TTAATATAATA
1 TAAATATAATA
*
905742 -AAATA-ATTA
1 TAAATATAATA
905751 -AAATATAATA
1 TAAATATAATA
905761 TAAATAAATAATA
1 TAAAT--ATAATA
905774 TAAATATAATA
1 TAAATATAATA
905785 TAAATAT
1 TAAATAT
905792 GTGAATATAT
Statistics
Matches: 62, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
9 8 0.13
10 7 0.11
11 27 0.44
13 20 0.32
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (11 bp):
TAAATATAATA
Found at i:905823 original size:17 final size:17
Alignment explanation
Indices: 905803--905857 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
905793 TGAATATATC
905803 AAATTTTATAATTACAT
1 AAATTTTATAATTACAT
* *
905820 AAATTAT-TAA-TATAT
1 AAATTTTATAATTACAT
905835 CAAATTTTATAATTACAT
1 -AAATTTTATAATTACAT
905853 AAATT
1 AAATT
905858 ATTAACATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
15 4 0.13
16 9 0.29
17 14 0.45
18 4 0.13
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATTTTATAATTACAT
Found at i:905833 original size:33 final size:33
Alignment explanation
Indices: 905795--905878 Score: 150
Period size: 33 Copynumber: 2.5 Consensus size: 33
905785 TAAATATGTG
905795 AATATATCAAATTTTATAATTACATAAATTATT
1 AATATATCAAATTTTATAATTACATAAATTATT
905828 AATATATCAAATTTTATAATTACATAAATTATT
1 AATATATCAAATTTTATAATTACATAAATTATT
* *
905861 AACATATCAAAATTTATA
1 AATATATCAAATTTTATA
905879 TAAATTTAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (33 bp):
AATATATCAAATTTTATAATTACATAAATTATT
Found at i:906638 original size:18 final size:19
Alignment explanation
Indices: 906596--906640 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
906586 TGATGATCAC
*
906596 TTTAA-AGATCAATTCTTT
1 TTTAAGAGATCAATTCATT
906614 TTATAAGAGATCAATT-ATT
1 TT-TAAGAGATCAATTCATT
906633 TTTAAGAG
1 TTTAAGAG
906641 TGATTAATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 8 0.33
19 7 0.29
20 9 0.38
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.44
Consensus pattern (19 bp):
TTTAAGAGATCAATTCATT
Found at i:906956 original size:18 final size:19
Alignment explanation
Indices: 906920--906959 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
906910 AAAATTGATA
*
906920 ATTTATGTATTTATATTAT
1 ATTTATATATTTATATTAT
906939 ATTTATATATTT-TATTAT
1 ATTTATATATTTATATTAT
906957 ATT
1 ATT
906960 ATAATTATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
ATTTATATATTTATATTAT
Found at i:907446 original size:3 final size:3
Alignment explanation
Indices: 907438--907468 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
907428 ATATTTATAT
907438 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
907469 TTTTTATGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:909107 original size:17 final size:17
Alignment explanation
Indices: 909087--909133 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
909077 TAAAAGTGAC
909087 TAAATTGATATTACAAA
1 TAAATTGATATTACAAA
* *
909104 TAAATTGATATTATAAG
1 TAAATTGATATTACAAA
909121 TAAATTGATATTA
1 TAAATTGATATTA
909134 ATACAATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (17 bp):
TAAATTGATATTACAAA
Found at i:909734 original size:33 final size:32
Alignment explanation
Indices: 909695--909764 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
909685 AATAATTAAA
* *
909695 ATATAATAAAAATAAATATATATTTTAAAATTT
1 ATATAATAAAAATAAATA-AAATATTAAAATTT
* * *
909728 ATATAATATAAATTATTAAAATATTAAAATTT
1 ATATAATAAAAATAAATAAAATATTAAAATTT
909760 ATATA
1 ATATA
909765 TATATATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 17 0.53
33 15 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (32 bp):
ATATAATAAAAATAAATAAAATATTAAAATTT
Found at i:909769 original size:18 final size:18
Alignment explanation
Indices: 909710--909776 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 18
909700 ATAAAAATAA
*
909710 ATATATATTTTAAAATTT
1 ATATATATATTAAAATTT
909728 ATATA-ATA-T-AAA-TT
1 ATATATATATTAAAATTT
*
909742 AT-TAAAATATTAAAATTT
1 ATAT-ATATATTAAAATTT
909760 ATATATATATATAAAAT
1 ATATATATAT-TAAAAT
909777 ATTTTAATAC
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
13 1 0.03
14 5 0.12
15 6 0.15
16 2 0.05
17 5 0.12
18 14 0.35
19 7 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATATATATTAAAATTT
Found at i:911104 original size:17 final size:17
Alignment explanation
Indices: 911066--911123 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
911056 TTTTTTAAAT
*
911066 AATTAAATTTAGATATAA
1 AATTAAATTGA-ATATAA
*
911084 AATTAAATT-ATTATAAA
1 AATTAAATTGAATAT-AA
*
911101 AATTATATTGAATATAA
1 AATTAAATTGAATATAA
911118 AATTAA
1 AATTAA
911124 TTAATTAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
16 3 0.09
17 18 0.53
18 13 0.38
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (17 bp):
AATTAAATTGAATATAA
Found at i:911211 original size:19 final size:21
Alignment explanation
Indices: 911162--911211 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
911152 TAAAAATAAT
911162 AAAAATATAATATGATATGAA
1 AAAAATATAATATGATATGAA
* *
911183 AAATAATATAA-AT-ATATTAC
1 AAA-AATATAATATGATATGAA
911203 AAAAATATA
1 AAAAATATA
911212 TAAATATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 6 0.23
20 8 0.31
21 5 0.19
22 7 0.27
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (21 bp):
AAAAATATAATATGATATGAA
Found at i:911224 original size:19 final size:19
Alignment explanation
Indices: 911148--911225 Score: 72
Period size: 21 Copynumber: 4.1 Consensus size: 19
911138 ACATGAAAAT
*
911148 AATATAAAAATA-AT-AAA
1 AATATATAAATATATCAAA
* *
911165 AATATA-ATATGATATGAAA
1 AATATATAAAT-ATATCAAA
911184 AATAATATAAATATATTACAAA
1 AAT-ATATAAATATA-T-CAAA
911206 AATATATAAATATATCAAA
1 AATATATAAATATATCAAA
911225 A
1 A
911226 TACATAAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
16 3 0.06
17 7 0.14
18 2 0.04
19 11 0.22
20 7 0.14
21 15 0.29
22 6 0.12
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (19 bp):
AATATATAAATATATCAAA
Found at i:911980 original size:16 final size:16
Alignment explanation
Indices: 911959--911991 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
911949 TTATAATTAA
911959 AATTAAATAAAAAATT
1 AATTAAATAAAAAATT
*
911975 AATTAAATAAATAATT
1 AATTAAATAAAAAATT
911991 A
1 A
911992 TCTAAGTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATTAAATAAAAAATT
Found at i:912100 original size:32 final size:32
Alignment explanation
Indices: 912056--912118 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
912046 ATCAGTCTAC
* * *
912056 ATAACATAAATTATGAATGTATCAAAATTTAT
1 ATAAAATAAATTATGAACGTATAAAAATTTAT
*
912088 ATAAAATAAATTATTAACGTATAAAAATTTA
1 ATAAAATAAATTATGAACGTATAAAAATTTA
912119 GAATATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (32 bp):
ATAAAATAAATTATGAACGTATAAAAATTTAT
Found at i:912665 original size:19 final size:22
Alignment explanation
Indices: 912623--912671 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 22
912613 TTTTTTATTT
*
912623 ATTATTATTTAAGATAAATTTA
1 ATTATTATTTAAGATAAATATA
912645 ATTATTATTT-A-A-AAATATA
1 ATTATTATTTAAGATAAATATA
*
912664 ATTTTTAT
1 ATTATTAT
912672 AATTAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 13 0.52
20 1 0.04
21 1 0.04
22 10 0.40
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
ATTATTATTTAAGATAAATATA
Found at i:912671 original size:22 final size:22
Alignment explanation
Indices: 912619--912688 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
912609 CGGTTTTTTT
*
912619 ATTTATTATTATTT-AAGATAA
1 ATTTATTATTATTTAAAAATAA
912640 ATTTAATTATTATTTAAAAATATA
1 ATTT-ATTATTATTTAAAAATA-A
*
912664 ATTT-TTA-TAATTAATAAATAA
1 ATTTATTATTATTTAA-AAATAA
912685 ATTT
1 ATTT
912689 TACATATATA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
21 15 0.35
22 18 0.42
23 5 0.12
24 5 0.12
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (22 bp):
ATTTATTATTATTTAAAAATAA
Found at i:912933 original size:2 final size:2
Alignment explanation
Indices: 912926--912951 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
912916 AGCACGTGCT
912926 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
912952 GTCTTTTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:916340 original size:16 final size:16
Alignment explanation
Indices: 916319--916349 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
916309 AATATTTATA
916319 TATTTATATTTTATTT
1 TATTTATATTTTATTT
*
916335 TATTTATTTTTTATT
1 TATTTATATTTTATT
916350 ATAGTATTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TATTTATATTTTATTT
Found at i:916450 original size:20 final size:21
Alignment explanation
Indices: 916425--916470 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
916415 TTACATAATG
* *
916425 ATTTTAT-TTTTTTAAATAAA
1 ATTTTATATTTATCAAATAAA
*
916445 ATTTTATATTTATCAAATTAA
1 ATTTTATATTTATCAAATAAA
916466 ATTTT
1 ATTTT
916471 TTTATATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTTTATATTTATCAAATAAA
Found at i:917271 original size:21 final size:21
Alignment explanation
Indices: 917229--917271 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
917219 TACTACTTAT
*
917229 AATATTTAATCTTTCATCATA
1 AATATTTAATCTTTCATAATA
*
917250 AATATTTTATCTTTTCA-AATA
1 AATATTTAATC-TTTCATAATA
917271 A
1 A
917272 TCTACTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.49
Consensus pattern (21 bp):
AATATTTAATCTTTCATAATA
Found at i:917563 original size:20 final size:18
Alignment explanation
Indices: 917526--917564 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
917516 AATTATTTAA
917526 ATTTAATTATAATAATAT
1 ATTTAATTATAATAATAT
*
917544 ATTTATATTAATATTAATAT
1 ATTTA-ATT-ATAATAATAT
917564 A
1 A
917565 AAATATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 3 0.17
20 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTAATTATAATAATAT
Found at i:918064 original size:12 final size:12
Alignment explanation
Indices: 918024--918064 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
918014 TATGTAATTG
918024 TTTTTATATTAT
1 TTTTTATATTAT
* *
918036 ATTTTATTTTAT
1 TTTTTATATTAT
*
918048 TTTTTGTATTAT
1 TTTTTATATTAT
918060 TTTTT
1 TTTTT
918065 TGTGAATTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTTTATATTAT
Found at i:918339 original size:20 final size:21
Alignment explanation
Indices: 918304--918344 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
918294 AAATTATTTT
*
918304 TTTAAATATTTTTATTTAAAG
1 TTTAAATATATTTATTTAAAG
918325 TTTAAATA-ATTTATTTAAAG
1 TTTAAATATATTTATTTAAAG
918345 AGATTGATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (21 bp):
TTTAAATATATTTATTTAAAG
Found at i:924542 original size:18 final size:19
Alignment explanation
Indices: 924504--924544 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
924494 ATATTTAAAT
* *
924504 AATATATATTAAAATTTTA
1 AATATATATTAAAAATATA
924523 AATAT-TATTAAAAATATA
1 AATATATATTAAAAATATA
924541 AATA
1 AATA
924545 ATTTATCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATATATATTAAAAATATA
Found at i:925502 original size:16 final size:16
Alignment explanation
Indices: 925455--925505 Score: 84
Period size: 16 Copynumber: 3.2 Consensus size: 16
925445 GTCTATTTAG
* *
925455 GTTTAAGCATTTTCGG
1 GTTTAAGCTTTTTCGA
925471 GTTTAAGCTTTTTCGA
1 GTTTAAGCTTTTTCGA
925487 GTTTAAGCTTTTTCGA
1 GTTTAAGCTTTTTCGA
925503 GTT
1 GTT
925506 CATGTTTGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.18, C:0.12, G:0.22, T:0.49
Consensus pattern (16 bp):
GTTTAAGCTTTTTCGA
Found at i:926660 original size:22 final size:22
Alignment explanation
Indices: 926608--926650 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
926598 AAAACTCATA
*
926608 ATATAATTTATTTTTTGATAAG
1 ATATAATTTACTTTTTGATAAG
926630 ATATAATTTACTTTTTGATAA
1 ATATAATTTACTTTTTGATAA
926651 ATTATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.53
Consensus pattern (22 bp):
ATATAATTTACTTTTTGATAAG
Found at i:929551 original size:2 final size:2
Alignment explanation
Indices: 929544--929580 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
929534 TAAGAAACAA
*
929544 AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
929581 GTATTCCATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:933211 original size:52 final size:51
Alignment explanation
Indices: 933152--933285 Score: 169
Period size: 52 Copynumber: 2.6 Consensus size: 51
933142 AAATAACGAG
* * **
933152 GTTGGAGTATCCTCGATTGTGAAAAATTGATGTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGATG-TTTTAAAAATAAAATCGGA
* * * *
933204 GTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTAAAAATAAAATCGGG
1 GTTGGAGTATCCCCGATT-ATGAAAAATTGATGTTTTAAAAATAAAATCGGA
*
933256 GTTGGAGTATCCCCGATTATGAACAATTGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGA
933286 GAAACTTAAC
Statistics
Matches: 69, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
51 8 0.12
52 51 0.74
53 10 0.14
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAAAAATAAAATCGGA
Found at i:935660 original size:13 final size:13
Alignment explanation
Indices: 935642--935667 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
935632 ACAAAGATCG
935642 ATGTATCGATACA
1 ATGTATCGATACA
935655 ATGTATCGATACA
1 ATGTATCGATACA
935668 TTTCCTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:935678 original size:21 final size:21
Alignment explanation
Indices: 935654--935695 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
935644 GTATCGATAC
935654 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
935675 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
935696 GGCAGTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.43
Consensus pattern (21 bp):
AATGTATCGATACATTTCCTT
Found at i:938795 original size:16 final size:16
Alignment explanation
Indices: 938774--938808 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
938764 TGTTTTTCTT
938774 TTTTTC-TCTTCCTTTC
1 TTTTTCATCTT-CTTTC
938790 TTTTTCATCTTCTTTC
1 TTTTTCATCTTCTTTC
938806 TTT
1 TTT
938809 CTTACCTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTCATCTTCTTTC
Found at i:940125 original size:28 final size:28
Alignment explanation
Indices: 940079--940234 Score: 199
Period size: 28 Copynumber: 5.6 Consensus size: 28
940069 CACTAACTTG
*
940079 TGTGGGCTTTG-AAGAGATGCCACTAACT
1 TGTGGGCTTTGAAAG-GATGCCACTGACT
*
940107 TGTAGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
940135 TGTGGGCTTTGGAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
940163 CGTGGGCTTTGAAAAGG-TGCCACCGATT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* * *
940191 TGTGGACTTTAAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
940219 TGTGGGCTTTGAAAGG
1 TGTGGGCTTTGAAAGG
940235 GTGCTGTCGC
Statistics
Matches: 108, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
27 4 0.04
28 97 0.90
29 7 0.06
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:940221 original size:84 final size:84
Alignment explanation
Indices: 940080--940234 Score: 222
Period size: 84 Copynumber: 1.8 Consensus size: 84
940070 ACTAACTTGT
* * * *
940080 GTGGGCTTTGAAGAGATGCCACTAACTTGTAGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTT
1 GTGGGCTTTGAAAAGATGCCACCAACTTGTAGGCTTTAAAAAGATGCCACTGACTTGTGGGCTTT
*
940145 GGAAGGATGCCACTGACTC
66 GAAAGGATGCCACTGACTC
* * *
940164 GTGGGCTTTGAAAAGGTGCCACCGATTTGT-GGACTTTAAAAAGATGCCACTGACTTGTGGGCTT
1 GTGGGCTTTGAAAAGATGCCACCAACTTGTAGG-CTTTAAAAAGATGCCACTGACTTGTGGGCTT
940228 TGAAAGG
65 TGAAAGG
940235 GTGCTGTCGC
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
83 2 0.03
84 60 0.97
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (84 bp):
GTGGGCTTTGAAAAGATGCCACCAACTTGTAGGCTTTAAAAAGATGCCACTGACTTGTGGGCTTT
GAAAGGATGCCACTGACTC
Found at i:940827 original size:28 final size:28
Alignment explanation
Indices: 940787--940858 Score: 94
Period size: 27 Copynumber: 2.6 Consensus size: 28
940777 AATAAAGCCA
940787 GGGGTTGGAGTATCCCCTCGA-AAATAAC
1 GGGGTTGGAGTATCCCCT-GATAAATAAC
* * *
940815 GGGGTTGGAGTAT-CGCTGATGATTAAC
1 GGGGTTGGAGTATCCCCTGATAAATAAC
940842 GGGGTTGGAGTATCCCC
1 GGGGTTGGAGTATCCCC
940859 GATTGTGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 2 0.05
27 21 0.55
28 15 0.39
ACGTcount: A:0.22, C:0.18, G:0.35, T:0.25
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCTGATAAATAAC
Found at i:940934 original size:52 final size:52
Alignment explanation
Indices: 940843--941018 Score: 203
Period size: 52 Copynumber: 3.4 Consensus size: 52
940833 ATGATTAACG
** * *
940843 GGGTTGGAGTATCCCCGATT-GTGAAAAATTAGTGTTTTTGGAAATAAAATCT
1 GGGTTGGAGTATCCCCGATTAAAGGAAAATTAGTG-TTTTGGAAATAAAATCA
* * * * * *
940895 GAGTTGGAGTATCCCCAATTAAAGGAATATTGGTGTTTTGAAAATAAAACCA
1 GGGTTGGAGTATCCCCGATTAAAGGAAAATTAGTGTTTTGGAAATAAAATCA
** * *
940947 GGGTTGGAGTATCCCCGATT-GTGGAAAATTAGTGTTTTAGAAATAAAATCG
1 GGGTTGGAGTATCCCCGATTAAAGGAAAATTAGTGTTTTGGAAATAAAATCA
940998 GGGTTGGAGTATCCCCGATTA
1 GGGTTGGAGTATCCCCGATTA
941019 TGAAAAATTG
Statistics
Matches: 102, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
51 43 0.42
52 50 0.49
53 9 0.09
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.31
Consensus pattern (52 bp):
GGGTTGGAGTATCCCCGATTAAAGGAAAATTAGTGTTTTGGAAATAAAATCA
Found at i:941002 original size:51 final size:50
Alignment explanation
Indices: 940841--941027 Score: 221
Period size: 51 Copynumber: 3.6 Consensus size: 50
940831 TGATGATTAA
*
940841 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTTGGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTG-TTTT-GAAATAAAAT
* * * * * * * *
940893 CTGAGTTGGAGTATCCCCAATTAAAGGAATATTGGTGTTTTGAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATT-ATGAAAAATTAGTGTTTTG-AAATAAAAT
* * *
940945 CAGGGTTGGAGTATCCCCGATTGTGGAAAATTAGTGTTTTAGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTT-GAAATAAAAT
940996 CGGGGTTGGAGTATCCCCGATTATGAAAAATT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATT
941028 GAGAAACTTA
Statistics
Matches: 112, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
51 52 0.46
52 51 0.46
53 9 0.08
ACGTcount: A:0.33, C:0.11, G:0.25, T:0.31
Consensus pattern (50 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGAAATAAAAT
Found at i:943154 original size:13 final size:13
Alignment explanation
Indices: 943136--943161 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
943126 ACAAAGATCG
943136 ATGTATCGATACA
1 ATGTATCGATACA
943149 ATGTATCGATACA
1 ATGTATCGATACA
943162 TTTCCTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:943650 original size:32 final size:32
Alignment explanation
Indices: 943581--944707 Score: 1230
Period size: 32 Copynumber: 35.8 Consensus size: 32
943571 GCCACTGACT
* * *
943581 TGTGGGCTTTGAAA--AGATGCCATCAAC-T-
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
*
943609 TGTGGGCTTTGAAATGGGTTGCCACCGACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* * ** * *
943641 TGTGGGCTTTCAAATGAGTCACCACCGATTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* *
943673 TGTGGGCTTTGAAAT--GATGCCACCGAC-T-
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
943701 TGTGGGCTTTGAAATGGGTTGCCA-CAGACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCA-ACTTG
**
943733 TGTATGCTTTGAAATGGGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* *
943765 TGTGGGCTTTGAAATAGGTTGCCACCAACTTA
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* * *
943797 TGTGGGCTTTCAAATGAGTTGCCACCGACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* * * *
943829 TGTGGGCTTTCAAATGAGTTGCCATCGACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* *
943861 TGTGGGCTTTGAAAT--GATGCCACAAAC-T-
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* **
943889 TGTGGGCTTTGAAATGGTGTTGCCA-TAGACACG
1 TGTGGGCTTTGAAATGG-GTTGCCACCA-ACTTG
943922 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
943954 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* * *
943986 TGTGGGTTTTCAAATGAGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* * * * *
944018 TGTGGGTTTTCAAATGAGTTGCTATCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
*
944050 TGTGGGCTTTGAAATAGGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* * *
944082 TGTGGGCTTTGAAATAGGTAGCCACCAACTTA
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* * *
944114 TGTGGGCTTTCAAATGAGTTGCCACCGACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* * ***
944146 TGTGGGCTTTCAAATGAGTTGCCATTGACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
*
944178 TGTGGGCTTTGAAAT--GATGCCA-CAGAC-T-
1 TGTGGGCTTTGAAATGGGTTGCCACCA-ACTTG
* **
944206 TGTGGGCTTTGAAATGGTGTTGCCA-TAGACACG
1 TGTGGGCTTTGAAATGG-GTTGCCACCA-ACTTG
944239 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
944271 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* * *
944303 TGTGGGTTTTCAAATGAGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* * *
944335 TGTGGGTTTTCAAATGAGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
*
944367 TGTGGGCTTTGAAATAGGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* * ** *
944399 TGTAGGCTTTCAAATAAGTTGCCACTAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
** * *
944431 TGTGGGCTTCAAAAT--GATGCCACTAAC-T-
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
**
944459 TGTGGGCTTTGAAATTGGTGTTGCCACGGACTTG
1 TGTGGGCTTTGAAA-TGG-GTTGCCACCAACTTG
* *
944493 TGTGGGCTTTGAATTGGGTTGCCACCGACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
944525 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* * *
944557 TGTGGGCTTTCAAATGAGTTGCCACCGACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
944589 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* * *
944621 TGTGGGCTTTCAAATGAGTTGCCACCGACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
* * *
944653 TGTAGGCTTTGAAAT--GATGCCACTAAC-T-
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
*
944681 TCTGGGCTTTGAAATTGGTGTTGCCAC
1 TGTGGGCTTTGAAA-TGG-GTTGCCAC
944708 GGAGTTGTGG
Statistics
Matches: 954, Mismatches: 111, Indels: 64
0.84 0.10 0.06
Matches are distributed among these distances:
28 83 0.09
29 8 0.01
30 62 0.06
31 20 0.02
32 726 0.76
33 42 0.04
34 13 0.01
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (32 bp):
TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
Found at i:944180 original size:317 final size:316
Alignment explanation
Indices: 943609--944695 Score: 1549
Period size: 317 Copynumber: 3.4 Consensus size: 316
943599 GCCATCAACT
* * * ** * *
943609 TGTGGGCTTTGAAATGGGTTGCCACCGACTTGTGTGGGCTTTCAAATGAGTCACCACCGATTTGT
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTGTGTGGGCTTTGAAATGGGTTGCCACCAACTTGT
* * * *
943674 GTGGGCTTTGAAATGA--TGCCACCGAC-T-TGTGGGCTTTGAAATGGGTTGCCACAGACTTGTG
66 GTGGGCTTTCAAATGAGTTGCCACCAACTTGTGTGGGCTTTCAAATGAGTTGCCACA-ACTTGTG
** *
943735 TATGCTTTGAAATGGGTTGCCACCAACTTGTGTGGGCTTTGAAATAGGTTGCCACCAACTTATGT
130 TGGGCTTTGAAATAGGTTGCCACCAACTTGTGTGGGCTTTGAAATAGGTTGCCACCAACTTATGT
943800 GGGCTTTCAAATGAGTTGCCACCGACTTGTGTGGGCTTTCAAATGAGTTGCCATCGACTTGTGTG
195 GGGCTTTCAAATGAGTTGCCACCGACTTGTGTGGGCTTTCAAATGAGTTGCCATCGACTTGTGTG
*
943865 GGCTTTGAAATGATGCCACAAACTTGTGGGCTTTGAAATGGTGTTGCCATAGACACG
260 GGCTTTGAAATGATGCCACAGACTTGTGGGCTTTGAAATGGTGTTGCCATAGACACG
943922 TGTGGGCTTTGAAATGGGTTGCCACCAACTTGTGTGGGCTTTGAAATGGGTTGCCACCAACTTGT
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTGTGTGGGCTTTGAAATGGGTTGCCACCAACTTGT
* * *
943987 GTGGGTTTTCAAATGAGTTGCCACCAACTTGTGTGGGTTTTCAAATGAGTTGCTATCAACTTGTG
66 GTGGGCTTTCAAATGAGTTGCCACCAACTTGTGTGGGCTTTCAAATGAGTTGCCA-CAACTTGTG
*
944052 TGGGCTTTGAAATAGGTTGCCACCAACTTGTGTGGGCTTTGAAATAGGTAGCCACCAACTTATGT
130 TGGGCTTTGAAATAGGTTGCCACCAACTTGTGTGGGCTTTGAAATAGGTTGCCACCAACTTATGT
*
944117 GGGCTTTCAAATGAGTTGCCACCGACTTGTGTGGGCTTTCAAATGAGTTGCCATTGACTTGTGTG
195 GGGCTTTCAAATGAGTTGCCACCGACTTGTGTGGGCTTTCAAATGAGTTGCCATCGACTTGTGTG
944182 GGCTTTGAAATGATGCCACAGACTTGTGGGCTTTGAAATGGTGTTGCCATAGACACG
260 GGCTTTGAAATGATGCCACAGACTTGTGGGCTTTGAAATGGTGTTGCCATAGACACG
944239 TGTGGGCTTTGAAATGGGTTGCCACCAACTTGTGTGGGCTTTGAAATGGGTTGCCACCAACTTGT
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTGTGTGGGCTTTGAAATGGGTTGCCACCAACTTGT
* *
944304 GTGGGTTTTCAAATGAGTTGCCACCAACTTGTGTGGGTTTTCAAATGAGTTGCCACCAACTTGTG
66 GTGGGCTTTCAAATGAGTTGCCACCAACTTGTGTGGGCTTTCAAATGAGTTGCCA-CAACTTGTG
* * * * *
944369 TGGGCTTTGAAATAGGTTGCCACCAACTTGTGTAGGCTTTCAAATAAGTTGCCACTAACTTGTGT
130 TGGGCTTTGAAATAGGTTGCCACCAACTTGTGTGGGCTTTGAAATAGGTTGCCACCAACTTATGT
** * *
944434 GGGC-TTCAAAATGA--TGCCACTAAC-T-TGTGGGCTTTGAAATTGGTGTTGCCA-CGGACTTG
195 GGGCTTTC-AAATGAGTTGCCACCGACTTGTGTGGGCTTTCAAA-T-GAGTTGCCATC-GACTTG
* * * * **
944493 TGTGGGCTTTGAATTGGGTTGCCACCGACTTGTGTGGGCTTTGAAATGG-GTTGCCACCA-ACTT
256 TGTGGGCTTTGAAAT--GATGCCACAGAC-T-TGTGGGCTTTGAAATGGTGTTGCCA-TAGACAC
944556 G
316 G
* * *
944557 TGTGGGCTTTCAAATGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGGGTTGCCACCAACTTGT
1 TGTGGGCTTTGAAATGGGTTGCCACCAACTTGTGTGGGCTTTGAAATGGGTTGCCACCAACTTGT
* * * *
944622 GTGGGCTTTCAAATGAGTTGCCACCGACTTGTGTAGGCTTTGAAATGA--TGCCACTAAC-T-TC
66 GTGGGCTTTCAAATGAGTTGCCACCAACTTGTGTGGGCTTTCAAATGAGTTGCCAC-AACTTGTG
944683 TGGGCTTTGAAAT
130 TGGGCTTTGAAAT
944696 TGGTGTTGCC
Statistics
Matches: 711, Mismatches: 48, Indels: 29
0.90 0.06 0.04
Matches are distributed among these distances:
313 85 0.12
314 16 0.02
315 47 0.07
316 12 0.02
317 415 0.58
318 118 0.17
319 18 0.03
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.32
Consensus pattern (316 bp):
TGTGGGCTTTGAAATGGGTTGCCACCAACTTGTGTGGGCTTTGAAATGGGTTGCCACCAACTTGT
GTGGGCTTTCAAATGAGTTGCCACCAACTTGTGTGGGCTTTCAAATGAGTTGCCACAACTTGTGT
GGGCTTTGAAATAGGTTGCCACCAACTTGTGTGGGCTTTGAAATAGGTTGCCACCAACTTATGTG
GGCTTTCAAATGAGTTGCCACCGACTTGTGTGGGCTTTCAAATGAGTTGCCATCGACTTGTGTGG
GCTTTGAAATGATGCCACAGACTTGTGGGCTTTGAAATGGTGTTGCCATAGACACG
Found at i:944787 original size:28 final size:27
Alignment explanation
Indices: 944702--945133 Score: 492
Period size: 27 Copynumber: 15.7 Consensus size: 27
944692 AAATTGGTGT
* *
944702 TGCCACGGAGTTGTGGACTCAAAAGGA
1 TGCCACAGAGTTGTGGACTTAAAAGGA
944729 TGCCACAGAGTTGTGGACTTAAAAGGA
1 TGCCACAGAGTTGTGGACTTAAAAGGA
*
944756 TGCCACAGAGTTGTGGACTTTAAAA-CA
1 TGCCACAGAGTTGTGGAC-TTAAAAGGA
* * *
944783 GTGCCACAAAATTGTGGAATTAAAA-GA
1 -TGCCACAGAGTTGTGGACTTAAAAGGA
* *
944810 GTGCCATAGAGTTGTGGACTCTAAAAGAA
1 -TGCCACAGAGTTGTGGACT-TAAAAGGA
* * *
944839 CGCCACAGAGTTATGGACTTGAAATGGA
1 TGCCACAGAGTTGTGGACTT-AAAAGGA
* *
944867 TGCCCCAGAGTTGTGGACTTAAAAGGG
1 TGCCACAGAGTTGTGGACTTAAAAGGA
* *
944894 TACCA-TGAAGTTGTGGACTTAAAAGGA
1 TGCCACAG-AGTTGTGGACTTAAAAGGA
* *
944921 TGCCACTGAGTTGTGGACCTAAAAGGA
1 TGCCACAGAGTTGTGGACTTAAAAGGA
** *
944948 TGCCATGGAGTTGTGGACTTTAAAAGAA
1 TGCCACAGAGTTGTGGAC-TTAAAAGGA
* *
944976 TGCCACAGAGTTTTGGACTTGAAACGGA
1 TGCCACAGAGTTGTGGACTT-AAAAGGA
*
945004 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACAGAGTTGTGGACTTAAAAGGA
* *
945031 TGCCACGGAGTTGTGGACTTAAAAAGA
1 TGCCACAGAGTTGTGGACTTAAAAGGA
* *
945058 TGCCACAGAGTGGTGGACTTTAAAAGGG
1 TGCCACAGAGTTGTGGAC-TTAAAAGGA
*
945086 TGCCACGGAGTTGTGGACTTTAAAAGGA
1 TGCCACAGAGTTGTGGAC-TTAAAAGGA
*
945114 TGCCACGGAGTTGTGGACTT
1 TGCCACAGAGTTGTGGACTT
945134 TGAAAAGAAA
Statistics
Matches: 345, Mismatches: 50, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
26 1 0.00
27 181 0.52
28 162 0.47
29 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.24
Consensus pattern (27 bp):
TGCCACAGAGTTGTGGACTTAAAAGGA
Found at i:944806 original size:55 final size:54
Alignment explanation
Indices: 944702--945133 Score: 492
Period size: 55 Copynumber: 7.9 Consensus size: 54
944692 AAATTGGTGT
* *
944702 TGCCACGGAGTTGTGGACTCAAAAGGATGCCACAGAGTTGTGGACTTAAAAGGA
1 TGCCACAGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGACTTAAAAGGA
* * * *
944756 TGCCACAGAGTTGTGGACTTTAAAA-CAGTGCCACAAAATTGTGGAATTAAAA-GA
1 TGCCACAGAGTTGTGGAC-TTAAAAGGA-TGCCACAGAGTTGTGGACTTAAAAGGA
* * * * *
944810 GTGCCATAGAGTTGTGGACTCTAAAAGAACGCCACAGAGTTATGGACTTGAAATGGA
1 -TGCCACAGAGTTGTGGACT-TAAAAGGATGCCACAGAGTTGTGGACTT-AAAAGGA
* * * *
944867 TGCCCCAGAGTTGTGGACTTAAAAGGGTACCA-TGAAGTTGTGGACTTAAAAGGA
1 TGCCACAGAGTTGTGGACTTAAAAGGATGCCACAG-AGTTGTGGACTTAAAAGGA
* * ** *
944921 TGCCACTGAGTTGTGGACCTAAAAGGATGCCATGGAGTTGTGGACTTTAAAAGAA
1 TGCCACAGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGAC-TTAAAAGGA
* * *
944976 TGCCACAGAGTTTTGGACTTGAAACGGATGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACAGAGTTGTGGACTT-AAAAGGATGCCACAGAGTTGTGGACTTAAAAGGA
* * * *
945031 TGCCACGGAGTTGTGGACTTAAAAAGATGCCACAGAGTGGTGGACTTTAAAAGGG
1 TGCCACAGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGAC-TTAAAAGGA
* *
945086 TGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGACTT
1 TGCCACAGAGTTGTGGAC-TTAAAAGGATGCCACAGAGTTGTGGACTT
945134 TGAAAAGAAA
Statistics
Matches: 319, Mismatches: 46, Indels: 25
0.82 0.12 0.06
Matches are distributed among these distances:
54 87 0.27
55 163 0.51
56 67 0.21
57 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.24
Consensus pattern (54 bp):
TGCCACAGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGACTTAAAAGGA
Found at i:949403 original size:19 final size:20
Alignment explanation
Indices: 949379--949421 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
949369 GAATCCAGTG
* *
949379 ACCGGCCACCA-CGTCGGTC
1 ACCGGCAACCACCGTCGGCC
949398 ACCGGCAACCACCGTCGGCC
1 ACCGGCAACCACCGTCGGCC
949418 ACCG
1 ACCG
949422 TTCATCGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.19, C:0.49, G:0.26, T:0.07
Consensus pattern (20 bp):
ACCGGCAACCACCGTCGGCC
Found at i:950470 original size:48 final size:48
Alignment explanation
Indices: 950408--950539 Score: 167
Period size: 48 Copynumber: 2.8 Consensus size: 48
950398 AGAGGAATGT
** * *
950408 CAATGTGCCAATTCAAAGCCAACGACATTGAGGTAAGGGAAAAGTGGA
1 CAATGTGCTGATTCAAGGCCAACGACATTGAGCTAAGGGAAAAGTGGA
* * *
950456 TAATGTGCTGATTCAAGGCTAGA-GACATTGAGCTAAGGGAAAAGTTGA
1 CAATGTGCTGATTCAAGGCCA-ACGACATTGAGCTAAGGGAAAAGTGGA
* *
950504 CAATGTACTGATTCAAGGCCAGCGACATTGAGCTAA
1 CAATGTGCTGATTCAAGGCCAACGACATTGAGCTAA
950540 TAAAGGTGCC
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
48 70 0.99
49 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.21
Consensus pattern (48 bp):
CAATGTGCTGATTCAAGGCCAACGACATTGAGCTAAGGGAAAAGTGGA
Found at i:950710 original size:28 final size:28
Alignment explanation
Indices: 950663--950818 Score: 208
Period size: 28 Copynumber: 5.6 Consensus size: 28
950653 CACTAACTTG
950663 TGTGGGCTTTG-AAGAGATGCCACTGACT
1 TGTGGGCTTTGAAAG-GATGCCACTGACT
* *
950691 TGTAGGTTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
950719 TGTGGGCTTTGGAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
950747 CGTGGGCTTTGAAAAGG-TGCCACCGATT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* *
950775 TGTGGACTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
950803 TGTGGGCTTTGAAAGG
1 TGTGGGCTTTGAAAGG
950819 GTGCTGCCGC
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
27 4 0.04
28 98 0.90
29 7 0.06
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:950786 original size:84 final size:84
Alignment explanation
Indices: 950664--950818 Score: 231
Period size: 84 Copynumber: 1.8 Consensus size: 84
950654 ACTAACTTGT
* * * *
950664 GTGGGCTTTGAAGAGATGCCACTGACTTGTAGGTTTTGAAAGGATGCCACTGACTTGTGGGCTTT
1 GTGGGCTTTGAAAAGATGCCACCGACTTGTAGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTT
*
950729 GGAAGGATGCCACTGACTC
66 GAAAGGATGCCACTGACTC
* *
950748 GTGGGCTTTGAAAAGGTGCCACCGATTTGT-GGACTTTGAAAAGATGCCACTGACTTGTGGGCTT
1 GTGGGCTTTGAAAAGATGCCACCGACTTGTAGG-CTTTGAAAAGATGCCACTGACTTGTGGGCTT
950812 TGAAAGG
65 TGAAAGG
950819 GTGCTGCCGC
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
83 2 0.03
84 61 0.97
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (84 bp):
GTGGGCTTTGAAAAGATGCCACCGACTTGTAGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTT
GAAAGGATGCCACTGACTC
Found at i:951610 original size:51 final size:51
Alignment explanation
Indices: 951426--951611 Score: 257
Period size: 52 Copynumber: 3.6 Consensus size: 51
951416 GATGATTAAT
* * * *
951426 GGGGTTGTAGTATCCCCGATTGTGAAAAATTAGTGTTTTTGGAAATAAAATC
1 GGGGTTGGAGTATCCCCGATTATAAAAAATTAGTG-TTTTGGAAATAAAACC
* *
951478 GGAGTTGGAGTATCCCCGATTA-AACGAAAATTGGTGTTTTGGAAATAAAACC
1 GGGGTTGGAGTATCCCCGATTATAA--AAAATTAGTGTTTTGGAAATAAAACC
** *
951530 GGGGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTAGAAATAAAACC
1 GGGGTTGGAGTATCCCCGATTATAAAAAATTAGTGTTTTGGAAATAAAACC
951581 GGGGTTGGAGTATCCCCGATTATAAAAAATT
1 GGGGTTGGAGTATCCCCGATTATAAAAAATT
951612 GAGAAACTTA
Statistics
Matches: 118, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
51 54 0.46
52 55 0.47
53 9 0.08
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (51 bp):
GGGGTTGGAGTATCCCCGATTATAAAAAATTAGTGTTTTGGAAATAAAACC
Found at i:953742 original size:13 final size:13
Alignment explanation
Indices: 953724--953749 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
953714 ACAAAGATCG
953724 ATGTATCGATACA
1 ATGTATCGATACA
953737 ATGTATCGATACA
1 ATGTATCGATACA
953750 TTTTCTTGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:954219 original size:32 final size:32
Alignment explanation
Indices: 954178--954920 Score: 844
Period size: 32 Copynumber: 23.5 Consensus size: 32
954168 GCCATCAACT
954178 TGTGGGCTTTGAAATGGGTTGCCACCGACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCGACTTG
* * ** *
954210 TGTGGGCTTTCAAATGAGTCACCACCGATTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCGACTTG
* * *
954242 TGTGGGGTTTAAAAT--GATGCCACCGAC-T-
1 TGTGGGCTTTGAAATGGGTTGCCACCGACTTG
*
954270 TGTGGGCTTTGAAATGGGTTGCCACAGACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCGACTTG
* *
954302 TGTGTGCTTTGAAATGGGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCGACTTG
* * *
954334 TGTGGGCTTTGAAATAGGTTGCCACCAACTTA
1 TGTGGGCTTTGAAATGGGTTGCCACCGACTTG
* *
954366 TGTGGGCTTTTAAATGAGTTGCCACCGACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCGACTTG
* * *
954398 TGTGGGCTTTCAAATGAGTTGCCATCGACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCGACTTG
* *
954430 TGTGGGCTTTGAAAT--GATGCCACAGAC-T-
1 TGTGGGCTTTGAAATGGGTTGCCACCGACTTG
** **
954458 TGTGGGCTTTGAAATGGTGTTGCCATAGACACG
1 TGTGGGCTTTGAAATGG-GTTGCCACCGACTTG
*
954491 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCGACTTG
*
954523 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCGACTTG
* * * *
954555 TGTGGGTTTTCAAATGAGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCGACTTG
** * * *
954587 TGTGGATTTTCAAATGAGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCGACTTG
* *
954619 TGTGGGCTTTGAAATAGGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCGACTTG
* ** **
954651 TGTGGGCTTTCAAATAAGTTGCCACTAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCGACTTG
** * **
954683 TGTGGGCTTCAAAAT--GATGCCACTAAC-T-
1 TGTGGGCTTTGAAATGGGTTGCCACCGACTTG
*
954711 TGTGGGCTTTGAAATTGGTGTTGCCACGGACTTG
1 TGTGGGCTTTGAAA-TGG-GTTGCCACCGACTTG
*
954745 TGTGGGTTTTGAAATGGGTTGCCACCGACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCGACTTG
* *
954777 TGTGGGCTTTGAAATGGGTTACCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCGACTTG
* * *
954809 TGTGGGCTTTCAAATGAGTTGCCACTGACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCGACTTG
*
954841 TGTGGGCTTTGAAATGGGTTGCCACCAACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCGACTTG
* *
954873 TGTGGGCTTTCAAATGAGTTGCCACCGACTTG
1 TGTGGGCTTTGAAATGGGTTGCCACCGACTTG
*
954905 TGTAGGCTTTGAAATG
1 TGTGGGCTTTGAAATG
954921 ATGCCACTAA
Statistics
Matches: 617, Mismatches: 79, Indels: 30
0.85 0.11 0.04
Matches are distributed among these distances:
28 40 0.06
29 4 0.01
30 38 0.06
31 11 0.02
32 490 0.79
33 21 0.03
34 13 0.02
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (32 bp):
TGTGGGCTTTGAAATGGGTTGCCACCGACTTG
Found at i:955039 original size:28 final size:28
Alignment explanation
Indices: 954954--955365 Score: 468
Period size: 28 Copynumber: 14.9 Consensus size: 28
954944 AAATTGGTGT
*
954954 TGCCAC-GAAGTTGTGGAC-TCAAAAGGA
1 TGCCACAG-AGTTGTGGACTTTAAAAGGA
*
954981 TGCCATAGAGTTGTGGAC-TTAAAAGGA
1 TGCCACAGAGTTGTGGACTTTAAAAGGA
955008 TGCCACAGAGTTGTGGACTTTAAAA-GA
1 TGCCACAGAGTTGTGGACTTTAAAAGGA
* * *
955035 GTGCCACAGAATTGTGGA-ATTAAAAGAA
1 -TGCCACAGAGTTGTGGACTTTAAAAGGA
* *
955063 TGCCATAGAGTTGTGGACTTTAAAAGAA
1 TGCCACAGAGTTGTGGACTTTAAAAGGA
* * *
955091 CGCCACAGAGTTGTGGACTTGAAATGGA
1 TGCCACAGAGTTGTGGACTTTAAAAGGA
* * *
955119 TGCCCCAAAGTTGTGGAC-TTAAAAGGG
1 TGCCACAGAGTTGTGGACTTTAAAAGGA
* *
955146 TACCA-TGAAGTTGTGGAC-TTAAAAGGA
1 TGCCACAG-AGTTGTGGACTTTAAAAGGA
* *
955173 TGCCACGGAGTTGTGGACTTTAAAAGAA
1 TGCCACAGAGTTGTGGACTTTAAAAGGA
* * * *
955201 TGCCACGGAGTTTTGGACTTGAAACGGA
1 TGCCACAGAGTTGTGGACTTTAAAAGGA
*
955229 TGCCACAGAGTTGTGGAC-TTAAAAGGG
1 TGCCACAGAGTTGTGGACTTTAAAAGGA
*
955256 TGCCACGGAGTTGTGGAC-TTAAAAGGA
1 TGCCACAGAGTTGTGGACTTTAAAAGGA
*
955283 TGCCAC-GAAGTTGTGGACTTTAAAAGGG
1 TGCCACAG-AGTTGTGGACTTTAAAAGGA
*
955311 TGCCACGGAGTTGTGGACTTTAAAAGGA
1 TGCCACAGAGTTGTGGACTTTAAAAGGA
*
955339 TGCCACGGAGTTGTGGACTTTGAAAAG
1 TGCCACAGAGTTGTGGACTTT-AAAAG
955366 AAATTCCACT
Statistics
Matches: 332, Mismatches: 41, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
26 1 0.00
27 151 0.45
28 174 0.52
29 6 0.02
ACGTcount: A:0.32, C:0.15, G:0.30, T:0.24
Consensus pattern (28 bp):
TGCCACAGAGTTGTGGACTTTAAAAGGA
Found at i:955052 original size:55 final size:55
Alignment explanation
Indices: 954954--955366 Score: 489
Period size: 55 Copynumber: 7.5 Consensus size: 55
954944 AAATTGGTGT
* *
954954 TGCCAC-GAAGTTGTGGAC-TCAAAAG-GATGCCATAGAGTTGTGGACTTAAAAGGA
1 TGCCACAG-AGTTGTGGACTTTAAAAGAG-TGCCACAGAGTTGTGGACTTAAAAGGA
* * *
955008 TGCCACAGAGTTGTGGACTTTAAAAGAGTGCCACAGAATTGTGGAATTAAAAGAA
1 TGCCACAGAGTTGTGGACTTTAAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGA
* ** *
955063 TGCCATAGAGTTGTGGACTTTAAAAGAACGCCACAGAGTTGTGGACTTGAAATGGA
1 TGCCACAGAGTTGTGGACTTTAAAAGAGTGCCACAGAGTTGTGGACTT-AAAAGGA
* * * * *
955119 TGCCCCAAAGTTGTGGAC-TTAAAAGGGTACCA-TGAAGTTGTGGACTTAAAAGGA
1 TGCCACAGAGTTGTGGACTTTAAAAGAGTGCCACAG-AGTTGTGGACTTAAAAGGA
* * * * *
955173 TGCCACGGAGTTGTGGACTTTAAAAGAATGCCACGGAGTTTTGGACTTGAAACGGA
1 TGCCACAGAGTTGTGGACTTTAAAAGAGTGCCACAGAGTTGTGGACTT-AAAAGGA
* *
955229 TGCCACAGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGA
1 TGCCACAGAGTTGTGGACTTTAAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGA
* *
955283 TGCCAC-GAAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGA
1 TGCCACAG-AGTTGTGGACTTTAAAAGAGTGCCACAGAGTTGTGGAC-TTAAAAGGA
*
955339 TGCCACGGAGTTGTGGACTTTGAAAAGA
1 TGCCACAGAGTTGTGGACTTT-AAAAGA
955367 AATTCCACTG
Statistics
Matches: 310, Mismatches: 36, Indels: 23
0.84 0.10 0.06
Matches are distributed among these distances:
53 1 0.00
54 60 0.19
55 170 0.55
56 73 0.24
57 6 0.02
ACGTcount: A:0.32, C:0.15, G:0.30, T:0.24
Consensus pattern (55 bp):
TGCCACAGAGTTGTGGACTTTAAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGA
Found at i:966658 original size:17 final size:18
Alignment explanation
Indices: 966636--966679 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
966626 TTTCATATTT
*
966636 TTTTCTTTTTTC-TCTTC
1 TTTTCTTTCTTCATCTTC
966653 TTTTC-TTCTTCATCTTC
1 TTTTCTTTCTTCATCTTC
966670 -TTTCTTTCTT
1 TTTTCTTTCTT
966680 ACCTAACCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTCTTTCTTCATCTTC
Found at i:968685 original size:13 final size:13
Alignment explanation
Indices: 968667--968692 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
968657 CAATTTTTTG
968667 TGTATCGATACAT
1 TGTATCGATACAT
968680 TGTATCGATACAT
1 TGTATCGATACAT
968693 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:968703 original size:32 final size:33
Alignment explanation
Indices: 968647--968710 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
968637 TACAAGCCAA
*
968647 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATATTTTGTGTATCGATACAT
968680 TGTATCGATAC-ATATTTTGTGTATCGATACA
1 TGTATCGATACAATATTTTGTGTATCGATACA
968711 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.63
33 11 0.37
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (33 bp):
TGTATCGATACAATATTTTGTGTATCGATACAT
Found at i:968704 original size:19 final size:19
Alignment explanation
Indices: 968647--968710 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
968637 TACAAGCCAA
*
968647 TGTATCGATACAATTTTTTG
1 TGTATCGATAC-ATATTTTG
968667 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
968680 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
968699 TGTATCGATACA
1 TGTATCGATACA
968711 AGTTTGGCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.30
14 1 0.03
15 1 0.03
18 1 0.03
19 12 0.32
20 11 0.30
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:971276 original size:13 final size:13
Alignment explanation
Indices: 971258--971295 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
971248 ATAATCCCCC
971258 TGTATCGATACAG
1 TGTATCGATACAG
*
971271 TGTATCGATACAT
1 TGTATCGATACAG
971284 TGTATCGATACA
1 TGTATCGATACA
971296 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:973396 original size:15 final size:15
Alignment explanation
Indices: 973376--973406 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
973366 ATTTCGTTTG
*
973376 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
973391 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
973406 G
1 G
973407 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:977470 original size:13 final size:13
Alignment explanation
Indices: 977452--977477 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
977442 CAATTTTTTG
977452 TGTATCGATACAT
1 TGTATCGATACAT
977465 TGTATCGATACAT
1 TGTATCGATACAT
977478 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:977488 original size:32 final size:33
Alignment explanation
Indices: 977432--977495 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
977422 TACAAGCTAA
*
977432 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATATTTTGTGTATCGATACAT
977465 TGTATCGATAC-ATATTTTGTGTATCGATACA
1 TGTATCGATACAATATTTTGTGTATCGATACA
977496 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.63
33 11 0.37
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (33 bp):
TGTATCGATACAATATTTTGTGTATCGATACAT
Found at i:977489 original size:19 final size:19
Alignment explanation
Indices: 977432--977495 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
977422 TACAAGCTAA
*
977432 TGTATCGATACAATTTTTTG
1 TGTATCGATAC-ATATTTTG
977452 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
977465 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
977484 TGTATCGATACA
1 TGTATCGATACA
977496 AGTTTGGCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.30
14 1 0.03
15 1 0.03
18 1 0.03
19 12 0.32
20 11 0.30
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:984438 original size:84 final size:84
Alignment explanation
Indices: 984320--984529 Score: 384
Period size: 84 Copynumber: 2.5 Consensus size: 84
984310 TGACGAATTT
984320 AAAACAAGACCATCCTTGTATAAATGACTCAAGGTGTAATATTGACATACTTCACACACATCATT
1 AAAACAAGACCATCCTTGTATAAATGACTCAAGGTGTAATATTGACATACTTCACACACATCATT
984385 ATATTCAGAGACATGTGGC
66 ATATTCAGAGACATGTGGC
* *
984404 AAAACAAGACCATCCTTGTATAAATGACTTAAGGTGTAATATTGACATACTTCACACACATTATT
1 AAAACAAGACCATCCTTGTATAAATGACTCAAGGTGTAATATTGACATACTTCACACACATCATT
*
984469 ATATTTAGAGACATGTGGC
66 ATATTCAGAGACATGTGGC
*
984488 AAAACAAGACCATCCTTGTATAAATGACTCAAGATGTAATAT
1 AAAACAAGACCATCCTTGTATAAATGACTCAAGGTGTAATAT
984530 CCAACATATG
Statistics
Matches: 121, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 121 1.00
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.29
Consensus pattern (84 bp):
AAAACAAGACCATCCTTGTATAAATGACTCAAGGTGTAATATTGACATACTTCACACACATCATT
ATATTCAGAGACATGTGGC
Found at i:986779 original size:2 final size:2
Alignment explanation
Indices: 986768--986805 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
986758 AAATGGGTTG
986768 TA TA TA -A 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 TA TA T
986806 GTATGAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:990902 original size:26 final size:26
Alignment explanation
Indices: 990843--990902 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 26
990833 TTGAAACAAT
* *
990843 TTTATTTTATTATTTAATTTTTAGTT
1 TTTATTTTATAATTTAATTTTTAGTA
990869 TTTAATTTT-TAATTT-ATTTTTAAGTGA
1 TTT-ATTTTATAATTTAATTTTT-AGT-A
990896 TTTATTT
1 TTTATTT
990903 AAAGTGTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
25 6 0.21
26 15 0.52
27 8 0.28
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (26 bp):
TTTATTTTATAATTTAATTTTTAGTA
Found at i:994390 original size:3 final size:3
Alignment explanation
Indices: 994382--994424 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
994372 ATTATCCCAA
994382 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
994425 TAAGAAAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1003851 original size:21 final size:22
Alignment explanation
Indices: 1003827--1003870 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1003817 TTTCTTAGCT
*
1003827 TCAAAAACATTTT-TATTTAAG
1 TCAAAAACATTTTGTATTAAAG
*
1003848 TCAAAAATATTTTGTATTAAAG
1 TCAAAAACATTTTGTATTAAAG
1003870 T
1 T
1003871 ATGCATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (22 bp):
TCAAAAACATTTTGTATTAAAG
Found at i:1005838 original size:335 final size:334
Alignment explanation
Indices: 1005229--1005895 Score: 1147
Period size: 335 Copynumber: 2.0 Consensus size: 334
1005219 TCTTTAAACC
* *
1005229 TAAAACATAGGTTCAATGGCTACCGTTGGTAATGGTACAACACCATTATCACATTGCCCTAGGAT
1 TAAAACATAGGCTCAATAGCTACCGTTGGTAATGGTACAACACCATTATCACATTGCCCTAGGAT
*
1005294 TAACACCCTTCCAAGCTATGTATGGATATGCCTAACATAGGTTTTCTTAGGATGCTCACACTAAA
66 TAACACCCTTCCAAGCTATGTATGGATATGCCTAACATAGGTTTTCTTAGGATGCTAACACTAAA
* * *
1005359 GTTAAGATTGCTACTATTCAAGAATTGTTCAAAAAAAAGGCAATTAAGTAAATTCATGCAAGATC
131 GGTAAAATTGCTACTATTCAAGAATTCTTCAAAAAAAAGGCAATTAAGTAAATTCATGCAAGATC
1005424 AATTGCAAAAGGCTCAACAAAGAATGAAACATTACGTTGATAAGAATAGAACTAACAGAGAGTTT
196 AATTGCAAAAGGCTCAACAAAGAATGAAACATTACGTTGATAAGAATAGAACTAACAGAGAGTTT
1005489 CAAGATAAAGTCTACTTGAAATTGCAACCCTACAGATAGACAACTCTAGCCCTTCGTAAGAATGT
261 CAAGATAAAGTCTACTTGAAATTGCAACCCTACAGATAGACAACTCTAGCCCTTCGTAAGAATGT
1005554 CAAACTCCT
326 CAAACTCCT
* **
1005563 TAAAACAT-GGCTCAATAGCTACTGTTGGTGGTGGTACAACACCATTATCACATTGCCCTAGGAT
1 TAAAACATAGGCTCAATAGCTACCGTTGGTAATGGTACAACACCATTATCACATTGCCCTAGGAT
* *
1005627 TAACACCCTTCCAAGCTATGTATGGATGGTGCCTAACATGGGTTTTCTTAGGATGCTAACACTAA
66 TAACACCCTTCCAAGCTATGTATGGAT-ATGCCTAACATAGGTTTTCTTAGGATGCTAACACTAA
* *
1005692 AGGTAAAATTGCTACTATTCAAGAATTCTTGAAAAAAATAGGCAATTAAGTAAATTCATGCGAGA
130 AGGTAAAATTGCTACTATTCAAGAATTCTTCAAAAAAA-AGGCAATTAAGTAAATTCATGCAAGA
* * *
1005757 TCAATTGCAAAAGGCTCAACAAAGAATGAAACATTATGTTGATAAGAATAGAACTGATAGAGAGT
194 TCAATTGCAAAAGGCTCAACAAAGAATGAAACATTACGTTGATAAGAATAGAACTAACAGAGAGT
* *
1005822 TTCAAGATAAAGTCTACTTGAAATTGCAACCCTATAGATAGACAACTCTAGCCCTTTGTAAGAAT
259 TTCAAGATAAAGTCTACTTGAAATTGCAACCCTACAGATAGACAACTCTAGCCCTTCGTAAGAAT
1005887 GTCAAACTC
324 GTCAAACTC
1005896 TGTTCAAGGT
Statistics
Matches: 313, Mismatches: 18, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
333 78 0.25
334 76 0.24
335 159 0.51
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.27
Consensus pattern (334 bp):
TAAAACATAGGCTCAATAGCTACCGTTGGTAATGGTACAACACCATTATCACATTGCCCTAGGAT
TAACACCCTTCCAAGCTATGTATGGATATGCCTAACATAGGTTTTCTTAGGATGCTAACACTAAA
GGTAAAATTGCTACTATTCAAGAATTCTTCAAAAAAAAGGCAATTAAGTAAATTCATGCAAGATC
AATTGCAAAAGGCTCAACAAAGAATGAAACATTACGTTGATAAGAATAGAACTAACAGAGAGTTT
CAAGATAAAGTCTACTTGAAATTGCAACCCTACAGATAGACAACTCTAGCCCTTCGTAAGAATGT
CAAACTCCT
Found at i:1007958 original size:71 final size:71
Alignment explanation
Indices: 1007842--1007984 Score: 286
Period size: 71 Copynumber: 2.0 Consensus size: 71
1007832 GAATCTTTAG
1007842 ATATATAAGTGTGCGTACTTCACATTTTATTCGGTATATTTTTTTAAGAAGAAAATAATAATCTC
1 ATATATAAGTGTGCGTACTTCACATTTTATTCGGTATATTTTTTTAAGAAGAAAATAATAATCTC
1007907 ATGATA
66 ATGATA
1007913 ATATATAAGTGTGCGTACTTCACATTTTATTCGGTATATTTTTTTAAGAAGAAAATAATAATCTC
1 ATATATAAGTGTGCGTACTTCACATTTTATTCGGTATATTTTTTTAAGAAGAAAATAATAATCTC
1007978 ATGATA
66 ATGATA
1007984 A
1 A
1007985 GTAATATCAG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.41
Consensus pattern (71 bp):
ATATATAAGTGTGCGTACTTCACATTTTATTCGGTATATTTTTTTAAGAAGAAAATAATAATCTC
ATGATA
Found at i:1014733 original size:31 final size:29
Alignment explanation
Indices: 1014698--1014772 Score: 84
Period size: 28 Copynumber: 2.6 Consensus size: 29
1014688 TGTAATAATA
*
1014698 TATATATTTATATTATAATTTTTTAACATAT
1 TATATATTTATATTATAA-ATTTT-ACATAT
*
1014729 TATATATATT-TATT-TAAATTTTATATAT
1 TATATAT-TTATATTATAAATTTTACATAT
1014757 TATA-ATTTATATTATA
1 TATATATTTATATTATA
1014773 TATAAATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
26 2 0.05
27 6 0.15
28 11 0.28
29 4 0.10
30 3 0.08
31 11 0.28
32 2 0.05
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (29 bp):
TATATATTTATATTATAAATTTTACATAT
Found at i:1014752 original size:21 final size:22
Alignment explanation
Indices: 1014704--1014756 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 22
1014694 AATATATATA
1014704 TTTATATTATAATTTTTTAACAT
1 TTTATA-TATAATTTTTTAACAT
*
1014727 ATTATATAT-ATTTATTTAA-AT
1 TTTATATATAATTT-TTTAACAT
1014748 TTTATATAT
1 TTTATATAT
1014757 TATAATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 14 0.52
22 8 0.30
23 5 0.19
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTATATATAATTTTTTAACAT
Found at i:1014755 original size:19 final size:19
Alignment explanation
Indices: 1014710--1014776 Score: 57
Period size: 21 Copynumber: 3.4 Consensus size: 19
1014700 TATATTTATA
1014710 TTATA-ATTT-TTTAACATAT
1 TTATATATTTATTTAA-AT-T
1014729 TATATATATTTATTTAAATT
1 T-TATATATTTATTTAAATT
*
1014749 TTATATATTATAATTTATATT
1 TTATATATT-T-ATTTAAATT
*
1014770 ATATATA
1 TTATATA
1014777 AATTTTAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
19 9 0.22
20 7 0.17
21 20 0.49
22 5 0.12
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (19 bp):
TTATATATTTATTTAAATT
Found at i:1014768 original size:33 final size:32
Alignment explanation
Indices: 1014692--1014844 Score: 93
Period size: 32 Copynumber: 4.6 Consensus size: 32
1014682 TAATTTTGTA
* **
1014692 ATAATATATATATTTATATTATAATTTTTTAAC
1 ATAATTTATATATTTATATTA-AATTTTTTATT
1014725 AT-ATTATATATATTTAT-TTAAATTTTATATATT
1 ATAATT-TATATATTTATATTAAATTTT-T-TATT
* *
1014758 ATAATTTATAT-TATATA-TAAATTTTAATATTT
1 ATAATTTATATATTTATATTAAATTTT-TTA-TT
* *
1014790 ATATATGAATGATATATTTATGTT--ATTTTTTATT
1 ATA-AT---TTATATATTTATATTAAATTTTTTATT
1014824 ATAATTTATATTATATTATAT
1 ATAATTTATA-TAT-TTATAT
1014845 AATAATGTCA
Statistics
Matches: 95, Mismatches: 11, Indels: 29
0.70 0.08 0.21
Matches are distributed among these distances:
30 4 0.04
31 11 0.12
32 29 0.31
33 26 0.27
34 8 0.08
35 2 0.02
36 10 0.11
37 4 0.04
38 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.58
Consensus pattern (32 bp):
ATAATTTATATATTTATATTAAATTTTTTATT
Found at i:1014788 original size:31 final size:30
Alignment explanation
Indices: 1014693--1014787 Score: 90
Period size: 31 Copynumber: 3.2 Consensus size: 30
1014683 AATTTTGTAA
*
1014693 TAATATATATATTTATATTATA-AT--TTTT
1 TAATATATA-ATTTATATTATATATAAATTT
* * * *
1014721 TAACATATTATATATATT-TATTTAAATTT
1 TAATATATAATTTATATTATATATAAATTT
1014750 TATATATTATAATTTATATTATATATAAATTT
1 TA-ATA-TATAATTTATATTATATATAAATTT
1014782 TAATAT
1 TAATAT
1014788 TTATATATGA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
26 2 0.04
27 9 0.17
28 7 0.13
29 5 0.10
30 3 0.06
31 14 0.27
32 12 0.23
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (30 bp):
TAATATATAATTTATATTATATATAAATTT
Found at i:1014792 original size:16 final size:16
Alignment explanation
Indices: 1014743--1014792 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
1014733 TATATTTATT
1014743 TAAATTTT-ATATATTA
1 TAAATTTTAATAT-TTA
* *
1014759 T-AATTTATATTATATA
1 TAAATTT-TAATATTTA
1014775 TAAATTTTAATATTTA
1 TAAATTTTAATATTTA
1014791 TA
1 TA
1014793 TATGAATGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
15 5 0.19
16 14 0.52
17 8 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TAAATTTTAATATTTA
Found at i:1014845 original size:19 final size:19
Alignment explanation
Indices: 1014725--1014847 Score: 54
Period size: 19 Copynumber: 5.9 Consensus size: 19
1014715 ATTTTTTAAC
*
1014725 ATATTATA-TATATTTATTT
1 ATATTATATTATA-TAATTT
* *
1014744 AAATTTTATATATTATAATTT
1 ATATTATAT-TA-TATAATTT
1014765 ATATTATA-TATA-AATTTT
1 ATATTATATTATATAA-TTT
1014783 AATATTTATATATGAATGATATATTT
1 -ATA-TTATAT-T--AT-ATA-ATTT
* *
1014809 ATGTTATTTTTTATTATAATTT
1 ATATTA--TATTA-TATAATTT
1014831 ATATTATATTATATAAT
1 ATATTATATTATATAAT
1014848 AATGTCACAT
Statistics
Matches: 79, Mismatches: 9, Indels: 32
0.66 0.08 0.27
Matches are distributed among these distances:
17 2 0.03
18 5 0.06
19 17 0.22
20 9 0.11
21 13 0.16
22 12 0.15
23 4 0.05
24 6 0.08
25 4 0.05
26 6 0.08
27 1 0.01
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
ATATTATATTATATAATTT
Found at i:1016522 original size:6 final size:7
Alignment explanation
Indices: 1016487--1016536 Score: 55
Period size: 7 Copynumber: 6.4 Consensus size: 7
1016477 GATAAATAAA
1016487 ATTTTTT
1 ATTTTTT
1016494 ATTAATTATT
1 ATT--TT-TT
1016504 ATTTTTT
1 ATTTTTT
1016511 ATTTTTT
1 ATTTTTT
1016518 ATTTTTT
1 ATTTTTT
1016525 CATATTTTT
1 -AT-TTTTT
1016534 ATT
1 ATT
1016537 CAAAATATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
7 20 0.53
8 6 0.16
9 7 0.18
10 5 0.13
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (7 bp):
ATTTTTT
Found at i:1016532 original size:16 final size:14
Alignment explanation
Indices: 1016487--1016536 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 14
1016477 GATAAATAAA
1016487 ATTTTTTATTAATTATT
1 ATTTTTTATT--TT-TT
1016504 ATTTTTTATTTTTT
1 ATTTTTTATTTTTT
1016518 ATTTTTTCATATTTTT
1 ATTTTTT-AT-TTTTT
1016534 ATT
1 ATT
1016537 CAAAATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
14 9 0.29
15 4 0.13
16 8 0.26
17 10 0.32
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (14 bp):
ATTTTTTATTTTTT
Found at i:1020661 original size:20 final size:19
Alignment explanation
Indices: 1020633--1020707 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
1020623 TTTTACCCAG
1020633 ATGTATCGATACATTTAAGA
1 ATGTATCGATACATTTAA-A
* *
1020653 ATATATCGATACATTCATAA
1 ATGTATCGATACATTTA-AA
* *
1020673 ATGTATCGATATATTCTTAA
1 ATGTATCGATACATT-TAAA
1020693 ATGTATCGATACATT
1 ATGTATCGATACATT
1020708 ATGTCTTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 45 0.98
21 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.39
Consensus pattern (19 bp):
ATGTATCGATACATTTAAA
Found at i:1027761 original size:52 final size:52
Alignment explanation
Indices: 1027681--1027800 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
1027671 AAAAGTTACT
* *
1027681 TGCATGTATCGATATATTTAATAGTGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
*
1027733 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
1027785 TGCATGTATCGATACA
1 TGCATGTATCGATACA
1027801 AAGATCAGTG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (52 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
Done.