Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012468.1 Kokia drynarioides strain JFW-HI SEQ_127472, 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: 35197
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:1185 original size:24 final size:24
Alignment explanation
Indices: 1076--1186 Score: 107
Period size: 24 Copynumber: 4.6 Consensus size: 24
1066 TAGACTAATA
* * *
1076 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAC
* *
1100 AGAGTTTAA-TGGAAACAGATAAAT
1 AGAGTTTAACT-GAAACAAATAAAC
* *
1124 AGAGTTTAATTGAAAGAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* * **
1148 AAAGTTTAATTGAAACAGTTAAAC
1 AGAGTTTAACTGAAACAAATAAAC
1172 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
1187 GATTATTTCT
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
23 1 0.01
24 71 0.97
25 1 0.01
ACGTcount: A:0.50, C:0.07, G:0.16, T:0.26
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:1186 original size:48 final size:48
Alignment explanation
Indices: 1076--1188 Score: 145
Period size: 48 Copynumber: 2.4 Consensus size: 48
1066 TAGACTAATA
* * * * * *
1076 AGAGTTTGACTCAAACAAATAAATAGAGTTTAATGGAAACAGATAAAT
1 AGAGTTTAACTGAAAGAAATAAACAAAGTTTAATGGAAACAGATAAAC
* * *
1124 AGAGTTTAATTGAAAGAAATAAACAAAGTTTAATTGAAACAGTTAAAC
1 AGAGTTTAACTGAAAGAAATAAACAAAGTTTAATGGAAACAGATAAAC
1172 AGAGTTTAACTGAAAGA
1 AGAGTTTAACTGAAAGA
1189 TTATTTCTCA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.26
Consensus pattern (48 bp):
AGAGTTTAACTGAAAGAAATAAACAAAGTTTAATGGAAACAGATAAAC
Found at i:5618 original size:17 final size:17
Alignment explanation
Indices: 5583--5621 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
5573 AGGTGAAGAA
** *
5583 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAAAGAATT
5600 CTTGTTCGTAAAGAATT
1 CTTGTTCGTAAAGAATT
5617 CTTGT
1 CTTGT
5622 CAAGGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAAAGAATT
Found at i:6584 original size:96 final size:96
Alignment explanation
Indices: 6417--6591 Score: 239
Period size: 96 Copynumber: 1.8 Consensus size: 96
6407 TTTGATTATC
** * *
6417 TCGATTTGAAGAAAGGTTTCACCTAGTAAGTTAAGGCACAATATTTCAGAATCGAAGATAAGGAA
1 TCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCAGAATCGAAGATAAAGAA
6482 ACATTGCCTCGATTAAGGGTATTCGACTATT
66 ACATTGCCTCGATTAAGGGTATTCGACTATT
**
6513 TCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAA-ATTTTTGAAACTCGAAG-TAAA-
1 TCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCAG-AA-TCGAAGATAAAG
*
6575 AGAATATTGCCTCGATT
64 A-AACATTGCCTCGATT
6592 TTAAAGTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
95 6 0.09
96 57 0.83
97 6 0.09
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.29
Consensus pattern (96 bp):
TCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCAGAATCGAAGATAAAGAA
ACATTGCCTCGATTAAGGGTATTCGACTATT
Found at i:7035 original size:30 final size:29
Alignment explanation
Indices: 6966--7228 Score: 316
Period size: 30 Copynumber: 9.0 Consensus size: 29
6956 TGAACATCTG
* * *
6966 GGGGT-AAAATGAAAATTTTGGAAGTTTA
1 GGGGTAAAAATGGAATTTTTGGAAGTTTT
*
6994 GGGGTAAAAATGGAACTTTTGGAAGTTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTTT
* *
7023 GAGGTCAAAAATGGAATTTTTGAAAGTTTT
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTT
*
7053 GGGGTCAAAAATGGAATTTTTTGAAGTTTT
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTT
* * *
7083 GGGGTCAAAAATGGATTTTTTTGAAG-TTC
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTT
* *
7112 GAGGGT-AAAATGGATTTTTTGGAAGTTTC
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTT
* * *
7141 GGGGTTAAAATGGAATTTTTGCAAGTTTA
1 GGGGTAAAAATGGAATTTTTGGAAGTTTT
7170 GGGGTAAAAATGGAATTTTTGGAAGTTTTT
1 GGGGTAAAAATGGAATTTTTGGAAG-TTTT
7200 GGGGTAAAAATGGAATTTTTGGATAGTTT
1 GGGGTAAAAATGGAATTTTTGGA-AGTTT
7229 AGGGACCTTC
Statistics
Matches: 210, Mismatches: 18, Indels: 12
0.88 0.08 0.05
Matches are distributed among these distances:
28 27 0.13
29 74 0.35
30 107 0.51
31 2 0.01
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.37
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTT
Found at i:7954 original size:77 final size:77
Alignment explanation
Indices: 7827--7988 Score: 297
Period size: 77 Copynumber: 2.1 Consensus size: 77
7817 CGTAGGGCGA
7827 CACGCGCCGTCGTCACCGCGCCTGGTCATGCGCGCCCATCCGACCACTCCTCCATCGTCGCTTTT
1 CACGCGCCGTCGTCACCGCGCCTGGTCATGCGCGCCCATCCGACCACTCCTCCATCGTCGCTTTT
7892 CCTCCCATGCGC
66 CCTCCCATGCGC
* * *
7904 CACGCGTCGTCGTCACCGCGCCTGGTCATGCGTGCCCGTCCGACCACTCCTCCATCGTCGCTTTT
1 CACGCGCCGTCGTCACCGCGCCTGGTCATGCGCGCCCATCCGACCACTCCTCCATCGTCGCTTTT
7969 CCTCCCATGCGC
66 CCTCCCATGCGC
7981 CACGCGCC
1 CACGCGCC
7989 TCCGATCGGT
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
77 81 1.00
ACGTcount: A:0.10, C:0.48, G:0.22, T:0.21
Consensus pattern (77 bp):
CACGCGCCGTCGTCACCGCGCCTGGTCATGCGCGCCCATCCGACCACTCCTCCATCGTCGCTTTT
CCTCCCATGCGC
Found at i:9119 original size:24 final size:23
Alignment explanation
Indices: 9082--9127 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
9072 ATTGGACTTG
*
9082 ATTTAAATAGATTTAAACTTTAA
1 ATTTAAATAAATTTAAACTTTAA
*
9105 ATTTATAATAAATTTAAATTTTA
1 ATTTA-AATAAATTTAAACTTTA
9128 TGTAAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
ATTTAAATAAATTTAAACTTTAA
Found at i:9120 original size:17 final size:17
Alignment explanation
Indices: 9095--9140 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
9085 TAAATAGATT
9095 TAAACTTTAAA-TTTATAA
1 TAAA-TTTAAATTTTAT-A
*
9113 TAAATTTAAATTTTATG
1 TAAATTTAAATTTTATA
9130 TAAATTTAAAT
1 TAAATTTAAAT
9141 CCTGTTGGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 17 0.65
18 9 0.35
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (17 bp):
TAAATTTAAATTTTATA
Found at i:9821 original size:205 final size:205
Alignment explanation
Indices: 9469--9978 Score: 869
Period size: 205 Copynumber: 2.5 Consensus size: 205
9459 ACTTGGCCTT
* * *
9469 CTTCTCAGTATCTTATCAGGAAGCTAATCTTTTATTGCTTTGACCTGCTTCTCGGTGTCTCATCA
1 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCGGTGTCTCATCA
9534 GGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTAATTTGGTCTTCTTCTCAATAT
66 GGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTAATTTGGTCTTCTTCTCAATAT
9599 CTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTGTACCTCATCAAGAAGACGA
131 CTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTGTACCTCATCAAGAAGACGA
*
9664 ATTTGTTCCA
196 ATTTGGTCCA
9674 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCGGTGTCTCATCA
1 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCGGTGTCTCATCA
* * *
9739 GGAAGCTGGGGTTTGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTAT
66 GGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTAATTTGGTCTTCTTCTCAATAT
*
9804 CTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTGTACCTCATCAGGAAGACGA
131 CTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTGTACCTCATCAAGAAGACGA
9869 ATTTGGTCCA
196 ATTTGGTCCA
* ** *
9879 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTGTTGCTTCG-CCATGCTTCTCAATATCTCATC
1 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACC-TGCTTCTCGGTGTCTCATC
* * *
9943 AAGAAGCTGGGATTCAAAGATTTGCTCACATCGAGC
65 AGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGC
9979 CCTGAGTTGG
Statistics
Matches: 288, Mismatches: 16, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
204 2 0.01
205 286 0.99
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (205 bp):
CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCGGTGTCTCATCA
GGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTAATTTGGTCTTCTTCTCAATAT
CTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCCGCTTCTCTGTACCTCATCAAGAAGACGA
ATTTGGTCCA
Found at i:26643 original size:29 final size:30
Alignment explanation
Indices: 26595--27096 Score: 319
Period size: 29 Copynumber: 17.4 Consensus size: 30
26585 TCTCGGGGGC
* *
26595 AAAATGGTGATTTTGGGACAGTTTG-GGGTTA
1 AAAATGG-AATTTTTGGA-AGTTTGAGGGTTA
* *
26626 AAAATGG-ATTTTTAGACA-TTCGAGGG-T-
1 AAAATGGAATTTTTGGA-AGTTTGAGGGTTA
* *
26653 AAAAGGGTAA-TTTT-GAGAGTTTTGA-GGTAA
1 AAAATGG-AATTTTTGGA-AG-TTTGAGGGTTA
* **
26683 AAAATGGAGTTTTTGGACA-TCCGAGGG-T-
1 AAAATGGAATTTTTGGA-AGTTTGAGGGTTA
* * *
26711 GAAATGGTAATTTTTGAAAGTTTCG-GGGTCA
1 AAAATGG-AATTTTTGGAAGTTT-GAGGGTTA
* * * *
26742 AAATTGGAAATTTTGGAGGTTTG-GGGGTA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTTA
* ** *
26771 AAAATGGAACTTTTGGAAGTTTTG-GCATCA
1 AAAATGGAATTTTTGGAAG-TTTGAGGGTTA
* * * * *
26801 AAAAAGGATTTTTTGGAAGTTTCAAGGTCA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTTA
26831 AAAATGGAATTTTTGGAAGTTTGAGGGTTA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTTA
*
26861 AAAATGGAATTTTTGGAAGTTCGAGGG-TA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTTA
* *
26890 AAAATGGAATTTTTCGAAGTTCGAGGG-TA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTTA
* * *
26919 AAAAT-GAAATTTTAGAAGTTTGAGGG-TG
1 AAAATGGAATTTTTGGAAGTTTGAGGGTTA
* *
26947 AAAATGGAA-TTTTGGAAGTTTTAGGGTCA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTTA
*
26976 AAAACGGAA--TTT-----TTT--GGGTTA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTTA
* *
26997 AAAATGGAATTTATGGAAGTTCGAGGG-TA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTTA
* * *
27026 AAAATGGAATTTTTTGAAGTTTTAGGGTCA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTTA
* * *
27056 AAAATGGAA-TTTTGAAAGTTCG-GGGGTA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTTA
27084 AAAATGGAATTTT
1 AAAATGGAATTTT
27097 CGAATAGTTT
Statistics
Matches: 370, Mismatches: 71, Indels: 62
0.74 0.14 0.12
Matches are distributed among these distances:
21 13 0.04
23 5 0.01
27 9 0.02
28 74 0.20
29 140 0.38
30 114 0.31
31 15 0.04
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTGAGGGTTA
Found at i:26769 original size:30 final size:30
Alignment explanation
Indices: 26712--27096 Score: 342
Period size: 29 Copynumber: 13.4 Consensus size: 30
26702 TCCGAGGGTG
*
26712 AAATGGTAATTTTTGAAAGTTTCG-GGGTCAA
1 AAATGG-AATTTTTGGAAGTTT-GAGGGTCAA
* * * *
26743 AATTGGAAATTTTGGAGGTTTGGGGGT-AA
1 AAATGGAATTTTTGGAAGTTTGAGGGTCAA
* **
26772 AAATGGAACTTTTGGAAGTTTTG-GCATCAA
1 AAATGGAATTTTTGGAAG-TTTGAGGGTCAA
* * * *
26802 AAAAGGATTTTTTGGAAGTTTCAAGGTCAA
1 AAATGGAATTTTTGGAAGTTTGAGGGTCAA
*
26832 AAATGGAATTTTTGGAAGTTTGAGGGTTAA
1 AAATGGAATTTTTGGAAGTTTGAGGGTCAA
*
26862 AAATGGAATTTTTGGAAGTTCGAGGGT-AA
1 AAATGGAATTTTTGGAAGTTTGAGGGTCAA
* *
26891 AAATGGAATTTTTCGAAGTTCGAGGGT-AA
1 AAATGGAATTTTTGGAAGTTTGAGGGTCAA
* * *
26920 AAAT-GAAATTTTAGAAGTTTGAGGGT-GA
1 AAATGGAATTTTTGGAAGTTTGAGGGTCAA
*
26948 AAATGGAA-TTTTGGAAGTTTTAGGGTCAA
1 AAATGGAATTTTTGGAAGTTTGAGGGTCAA
* *
26977 AAACGGAA--TTT-----TTT--GGGTTAA
1 AAATGGAATTTTTGGAAGTTTGAGGGTCAA
* *
26998 AAATGGAATTTATGGAAGTTCGAGGGT-AA
1 AAATGGAATTTTTGGAAGTTTGAGGGTCAA
* *
27027 AAATGGAATTTTTTGAAGTTTTAGGGTCAA
1 AAATGGAATTTTTGGAAGTTTGAGGGTCAA
* * *
27057 AAATGGAA-TTTTGAAAGTTCGGGGGT-AA
1 AAATGGAATTTTTGGAAGTTTGAGGGTCAA
27085 AAATGGAATTTT
1 AAATGGAATTTT
27097 CGAATAGTTT
Statistics
Matches: 293, Mismatches: 44, Indels: 36
0.79 0.12 0.10
Matches are distributed among these distances:
21 13 0.04
23 5 0.02
28 55 0.19
29 109 0.37
30 106 0.36
31 5 0.02
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.34
Consensus pattern (30 bp):
AAATGGAATTTTTGGAAGTTTGAGGGTCAA
Found at i:26785 original size:59 final size:59
Alignment explanation
Indices: 26712--27096 Score: 322
Period size: 59 Copynumber: 6.7 Consensus size: 59
26702 TCCGAGGGTG
* * * *
26712 AAATGGTAATTTTTGAAAGTTTCGGGGTCAAAATTGGAAATTTTGGAGGTTTGGGGGTAA
1 AAATGG-AATTTTTGGAAGTTTCGGGGTCAAAAATGGAAATTTTGGAAGTTTGAGGGTAA
* * ** * ** * *
26772 AAATGGAACTTTTGGAAGTTTTGGCATCAAAAAAGGATTTTTTGGAAGTTTCAAGGTCAA
1 AAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAAATTTTGGAAGTTTGAGGGT-AA
* * *
26832 AAATGGAATTTTTGGAAGTTT-GAGGGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTAA
1 AAATGGAATTTTTGGAAGTTTCG-GGGTCAAAAATGGAAATTTTGGAAGTTTGAGGGTAA
* * *
26891 AAATGGAATTTTTCGAAG-TTCGAGGGT-AAAAAT-GAAATTTTAGAAGTTTGAGGGTGA
1 AAATGGAATTTTTGGAAGTTTCG-GGGTCAAAAATGGAAATTTTGGAAGTTTGAGGGTAA
** * *
26948 AAATGGAA-TTTTGGAAGTTTTAGGGTCAAAAACGG-AA-TTT-----TTTG-GGTTAA
1 AAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAAATTTTGGAAGTTTGAGGGTAA
* * * *
26998 AAATGGAATTTATGGAAG-TTCGAGGGT-AAAAATGGAATTTTTTGAAGTTTTAGGGTCAA
1 AAATGGAATTTTTGGAAGTTTCG-GGGTCAAAAATGGAAATTTTGGAAGTTTGAGGGT-AA
*
27057 AAATGGAA-TTTTGAAAG-TTCGGGGGT-AAAAATGG-AATTTT
1 AAATGGAATTTTTGGAAGTTTC-GGGGTCAAAAATGGAAATTTT
27097 CGAATAGTTT
Statistics
Matches: 264, Mismatches: 43, Indels: 39
0.76 0.12 0.11
Matches are distributed among these distances:
50 21 0.08
51 17 0.06
52 3 0.01
56 15 0.06
57 45 0.17
58 34 0.13
59 75 0.28
60 54 0.20
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.34
Consensus pattern (59 bp):
AAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAAATTTTGGAAGTTTGAGGGTAA
Found at i:26849 original size:60 final size:60
Alignment explanation
Indices: 26767--26989 Score: 192
Period size: 60 Copynumber: 3.8 Consensus size: 60
26757 GAGGTTTGGG
* *
26767 GGTAAAAATGGAACTTTTGGAAGTTTTG-GCATCAAAAAAGGATTTTTTGGAAGTTTC-AA
1 GGTAAAAATGGAATTTTTGGAAGTTTTGAGCATCAAAAAAGGAATTTTTGGAAG-TTCGAA
** * * *
26826 GGTCAAAAATGGAATTTTTGGAAG-TTTGAGGGTTAAAAATGGAATTTTTGGAAGTTCGAG
1 GGT-AAAAATGGAATTTTTGGAAGTTTTGAGCATCAAAAAAGGAATTTTTGGAAGTTCGAA
* * ** * * * * *
26886 GGTAAAAATGGAATTTTTCGAAG-TTCGAGGGT--AAAAATGAAATTTTAGAAGTTTGAG
1 GGTAAAAATGGAATTTTTGGAAGTTTTGAGCATCAAAAAAGGAATTTTTGGAAGTTCGAA
* ** *
26943 GGTGAAAATGGAA-TTTTGGAAGTTTT-AGGGTCAAAAACGGAATTTTT
1 GGTAAAAATGGAATTTTTGGAAGTTTTGAGCATCAAAAAAGGAATTTTT
26990 TGGGTTAAAA
Statistics
Matches: 138, Mismatches: 20, Indels: 13
0.81 0.12 0.08
Matches are distributed among these distances:
56 13 0.09
57 34 0.25
58 11 0.08
59 37 0.27
60 43 0.31
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.33
Consensus pattern (60 bp):
GGTAAAAATGGAATTTTTGGAAGTTTTGAGCATCAAAAAAGGAATTTTTGGAAGTTCGAA
Found at i:26989 original size:21 final size:21
Alignment explanation
Indices: 26960--27008 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
26950 ATGGAATTTT
*
26960 GGAAGTTTTAGGGTCAAAAAC
1 GGAATTTTTAGGGTCAAAAAC
* * *
26981 GGAATTTTTTGGGTTAAAAAT
1 GGAATTTTTAGGGTCAAAAAC
27002 GGAATTT
1 GGAATTT
27009 ATGGAAGTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.35
Consensus pattern (21 bp):
GGAATTTTTAGGGTCAAAAAC
Found at i:27030 original size:79 final size:79
Alignment explanation
Indices: 26917--27068 Score: 234
Period size: 80 Copynumber: 1.9 Consensus size: 79
26907 AGTTCGAGGG
* *
26917 TAAAAATGAAATTTTAGAAGTTTGAGGGTGAAAATGGAA-TTTTGGAAGTTTTAGGGTCAAAAAC
1 TAAAAATGAAATTTTAGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAAC
26981 GGAATTTTTTGGGT
66 GGAATTTTTTGGGT
* * *
26995 TAAAAATGGAATTTATGGAAGTTCGAGGGTAAAAATGGAATTTTTTGAAGTTTTAGGGTCAAAAA
1 TAAAAATGAAATTT-TAGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAA
*
27060 TGGAATTTT
65 CGGAATTTT
27069 GAAAGTTCGG
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
78 13 0.20
79 22 0.33
80 31 0.47
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.35
Consensus pattern (79 bp):
TAAAAATGAAATTTTAGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAAC
GGAATTTTTTGGGT
Found at i:27114 original size:107 final size:106
Alignment explanation
Indices: 26888--27102 Score: 245
Period size: 107 Copynumber: 2.0 Consensus size: 106
26878 AGTTCGAGGG
* * *
26888 TAAAAATGGAATTTTTCGAAGTTCGAGGGTAAAAATGAAATTTTAGAAGTTTGAGGGTGAAAATG
1 TAAAAAGGGAATTTATCGAAGTTCGAGGGTAAAAATGAAATTTTAGAAGTTTGAGGGTAAAAATG
* ** * **
26953 GAATTTTGGAAGTTTTAGGGTCAAAAACGGAATTTTTTGGGT
66 GAATTTTGAAAGTTCGAGGGTCAAAAACGGAA-TTTTTCGAA
* * * * *
26995 TAAAAATGGAATTTATGGAAGTTCGAGGGTAAAAATGGAATTTTTTGAAGTTTTAGGGTCAAAAA
1 TAAAAAGGGAATTTATCGAAGTTCGAGGGTAAAAAT-GAAATTTTAGAAGTTTGAGGGT-AAAAA
* *
27060 TGGAATTTTGAAAGTTCGGGGGT-AAAAATGGAA-TTTTCGAA
64 TGGAATTTTGAAAGTTCGAGGGTCAAAAACGGAATTTTTCGAA
27101 TA
1 TA
27103 GTTTAGGGAA
Statistics
Matches: 92, Mismatches: 14, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
106 7 0.08
107 34 0.37
108 28 0.30
109 23 0.25
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.33
Consensus pattern (106 bp):
TAAAAAGGGAATTTATCGAAGTTCGAGGGTAAAAATGAAATTTTAGAAGTTTGAGGGTAAAAATG
GAATTTTGAAAGTTCGAGGGTCAAAAACGGAATTTTTCGAA
Found at i:28136 original size:3 final size:3
Alignment explanation
Indices: 28075--28120 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
28065 AAAAAAATAC
* * *
28075 TTA TTA TTA TTA TTA ATA TTAA TTA ATA TTA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
28121 AAACAGTTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:28927 original size:24 final size:23
Alignment explanation
Indices: 28890--28936 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
28880 ATTGGACTTG
*
28890 ATTTAAATAGATTTAAACTTTAA
1 ATTTAAATAAATTTAAACTTTAA
*
28913 ATTTATAATAAATTTAAATTTTAA
1 ATTTA-AATAAATTTAAACTTTAA
28937 GTAAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTTAAATAAATTTAAACTTTAA
Found at i:28928 original size:17 final size:17
Alignment explanation
Indices: 28903--28982 Score: 106
Period size: 17 Copynumber: 4.6 Consensus size: 17
28893 TAAATAGATT
*
28903 TAAACTTTAAATTTATAA
1 TAAA-TTTAAATTTAAAA
* *
28921 TAAATTTAAATTTTAAG
1 TAAATTTAAATTTAAAA
*
28938 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
28955 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
28972 TAAATTTAAAT
1 TAAATTTAAAT
28983 ACTGTTGAGC
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
17 49 0.92
18 4 0.08
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:28930 original size:6 final size:6
Alignment explanation
Indices: 28900--28982 Score: 59
Period size: 6 Copynumber: 14.3 Consensus size: 6
28890 ATTTAAATAG
* *
28900 ATTTAA ACTTTAA ATTTATA A--TAA ATTTAA ATTTTA A-GTAA ATTTAA
1 ATTTAA A-TTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * * *
28947 ACTTAA A-ATAA ATTTAA TTTTAA A-ATAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT
28983 ACTGTTGAGC
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
4 2 0.03
5 13 0.22
6 36 0.61
7 8 0.14
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:30773 original size:31 final size:30
Alignment explanation
Indices: 30708--30774 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
30698 TTTTACTTTT
* **
30708 CCCCCAAAACTTTTACGCCTTCCCAGTTTC
1 CCCCCAAAACTTTTACGCCCTCCCAGTCCC
*
30738 CCCCCAAAACTTTTACTCACCTCCCA-TCCC
1 CCCCCAAAACTTTTACGC-CCTCCCAGTCCC
30768 ACCCCCA
1 -CCCCCA
30775 TCTACCTCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 19 0.61
31 12 0.39
ACGTcount: A:0.22, C:0.51, G:0.03, T:0.24
Consensus pattern (30 bp):
CCCCCAAAACTTTTACGCCCTCCCAGTCCC
Found at i:34585 original size:33 final size:33
Alignment explanation
Indices: 34547--34659 Score: 156
Period size: 33 Copynumber: 3.4 Consensus size: 33
34537 CTGCCTTGAG
* * *
34547 AGATGTTCGAATCAATGATGAAGTTG-CACTGAT
1 AGATGTTCCAATCATTGATGAAG-CGACACTGAT
* *
34580 TGATGTTCCAATCATTGATGAAGCGACGCTGAT
1 AGATGTTCCAATCATTGATGAAGCGACACTGAT
*
34613 AGATGTTCCAATCATTGATGAAGCGACGCTGAT
1 AGATGTTCCAATCATTGATGAAGCGACACTGAT
34646 AGATGTTCCAATCA
1 AGATGTTCCAATCA
34660 CTTATGTAGA
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
32 1 0.01
33 72 0.99
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (33 bp):
AGATGTTCCAATCATTGATGAAGCGACACTGAT
Found at i:34600 original size:66 final size:66
Alignment explanation
Indices: 34516--34659 Score: 159
Period size: 66 Copynumber: 2.2 Consensus size: 66
34506 GCCCTGACAA
* * *
34516 ATGTTCCAATGAATGATGAAACTG-C-CTTGAGAGATGTTCGAATCAATGATGAAGTTG-CACTG
1 ATGTTCCAATCAATGATGAAAC-GACGC-TGAGAGATGTTCCAATCAATGATGAAG-CGACACTG
*
34578 ATTG
63 ATAG
* * * * *
34582 ATGTTCCAATCATTGATGAAGCGACGCTGATAGATGTTCCAATCATTGATGAAGCGACGCTGATA
1 ATGTTCCAATCAATGATGAAACGACGCTGAGAGATGTTCCAATCAATGATGAAGCGACACTGATA
34647 G
66 G
34648 ATGTTCCAATCA
1 ATGTTCCAATCA
34660 CTTATGTAGA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
65 2 0.03
66 63 0.95
67 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (66 bp):
ATGTTCCAATCAATGATGAAACGACGCTGAGAGATGTTCCAATCAATGATGAAGCGACACTGATA
G
Done.