Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004600.1 Kokia drynarioides strain JFW-HI SEQ_118098, 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: 26739
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Found at i:2626 original size:28 final size:28
Alignment explanation
Indices: 2595--2656 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
2585 AAAATGAGAT
* *
2595 TTTTGGATACCCGGGGGTAAAATAGTAA
1 TTTTGGACACCCGGGGGCAAAATAGTAA
** * *
2623 TTTTGGACACTTGGGGGCAAAATGGTAG
1 TTTTGGACACCCGGGGGCAAAATAGTAA
2651 TTTTGG
1 TTTTGG
2657 GAATGTTCGG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.26, C:0.10, G:0.32, T:0.32
Consensus pattern (28 bp):
TTTTGGACACCCGGGGGCAAAATAGTAA
Found at i:2705 original size:59 final size:57
Alignment explanation
Indices: 2641--2858 Score: 163
Period size: 59 Copynumber: 3.7 Consensus size: 57
2631 ACTTGGGGGC
* * *
2641 AAAATGGTAGTTTTGGGAATGTTCGGGGTCAAAAATGGAATTTTCAAACATTCGAGGAT
1 AAAATGGTAATTTTAGGAAAGTT-GGGGTC-AAAATGGAATTTTCAAACATTCGAGGAT
** * * * * * *
2700 AAAATGGTAATTTTTTGAAAGTTTAGGGTTTAAAATGGAATTTTTAGACATTCGGGGGT
1 AAAATGGTAATTTTAGGAAAG-TT-GGGGTCAAAATGGAATTTTCAAACATTCGAGGAT
* * * * *
2759 AAAATAGTAATTTTAGGAAAATTGTGGTCAAAATGGAATTTT-AGGAA-TTTCGAGGGT
1 AAAATGGTAATTTTAGGAAAGTTGGGGTCAAAATGGAATTTTCA--AACATTCGAGGAT
* * * *
2816 AAATTGGTAACTTTT-GGAAAAATCGAGGTCAAAATGGAATTTT
1 AAAATGGTAA-TTTTAGG-AAAGTTGGGGTCAAAATGGAATTTT
2859 TGGGAGTTCT
Statistics
Matches: 129, Mismatches: 25, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
56 1 0.01
57 34 0.26
58 30 0.23
59 58 0.45
60 6 0.05
ACGTcount: A:0.36, C:0.06, G:0.25, T:0.34
Consensus pattern (57 bp):
AAAATGGTAATTTTAGGAAAGTTGGGGTCAAAATGGAATTTTCAAACATTCGAGGAT
Found at i:2842 original size:30 final size:30
Alignment explanation
Indices: 2692--3243 Score: 174
Period size: 29 Copynumber: 18.8 Consensus size: 30
2682 TTTCAAACAT
* * *
2692 TCGAGGATAAAATGGTAATTTTTTG-AAAG
1 TCGAGGGTAAAATGGTAATTTTTGGAAAAA
** * * *
2721 TTTAGGGTTTAAAATGG-AATTTTTAG-ACAT
1 TCGAGGG--TAAAATGGTAATTTTTGGAAAAA
* * *
2751 TCGGGGGTAAAATAGTAATTTTAGG-AAAA
1 TCGAGGGTAAAATGGTAATTTTTGGAAAAA
* * * **
2780 TTG-TGGTCAAAATGG-AATTTTAGG-AATT
1 TCGAGGGT-AAAATGGTAATTTTTGGAAAAA
* *
2808 TCGAGGGTAAATTGGTAACTTTTGGAAAAA
1 TCGAGGGTAAAATGGTAATTTTTGGAAAAA
* **
2838 TCGA-GGTCAAAATGG-AATTTTTGG-GAGT
1 TCGAGGGT-AAAATGGTAATTTTTGGAAAAA
* * * *
2866 TCTAGGGTAAAACGATAATTTTTAGAAAAA
1 TCGAGGGTAAAATGGTAATTTTTGGAAAAA
* **
2896 TC-AGGGTTAAAAAT-G-AAATTTTGGAAAGT
1 TCGAGGG-T-AAAATGGTAATTTTTGGAAAAA
*
2925 TCGAGGGTAAAGTGGTAATTTTTGGAAAAA
1 TCGAGGGTAAAATGGTAATTTTTGGAAAAA
* **
2955 TCGAGGTTAAAAATGG-AA-TTTTGGAAAGT
1 TCGAGGGT-AAAATGGTAATTTTTGGAAAAA
* *
2984 TAGAGGGTAAAATGGTAATTTTTTAGAAAAA
1 TCGAGGGTAAAATGGTAA-TTTTTGGAAAAA
** ** * **
3015 TAAAGGCCAAAAATAG-AA-TTTTGGAAAGT
1 TCGAGG-GTAAAATGGTAATTTTTGGAAAAA
* ***
3044 TCGAGGGTAAATTGGTAATTTTT-TTTAAA
1 TCGAGGGTAAAATGGTAATTTTTGGAAAAA
* ** *
3073 T-TAGGGTTAAAAATGG-AA-TCATGG-AAAG
1 TCGAGGG-T-AAAATGGTAATTTTTGGAAAAA
** *
3101 TTTAGGGTTAAAATGGTAATTTTTGCAAAAA
1 TCGAGGG-TAAAATGGTAATTTTTGGAAAAA
* * * **
3132 TC-AAGATCAAAAATAG-AA-TTTTGGAAAGT
1 TCGAGGGT--AAAATGGTAATTTTTGGAAAAA
3161 TC-AGGGGTAAAATGGTAATTTTTGGAAAAAA
1 TCGA-GGGTAAAATGGTAATTTTTGG-AAAAA
* * **
3192 T-TAGGGTCAAAAATAG-AA-TTTTGGAAAGT
1 TCGAGGGT--AAAATGGTAATTTTTGGAAAAA
3221 TCGAGGGTAAAAAT-GTAATTTTT
1 TCGAGGGT-AAAATGGTAATTTTT
3244 AAAAAGTTTA
Statistics
Matches: 379, Mismatches: 102, Indels: 83
0.67 0.18 0.15
Matches are distributed among these distances:
28 77 0.20
29 142 0.37
30 98 0.26
31 50 0.13
32 12 0.03
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.33
Consensus pattern (30 bp):
TCGAGGGTAAAATGGTAATTTTTGGAAAAA
Found at i:3100 original size:177 final size:176
Alignment explanation
Indices: 2667--3306 Score: 620
Period size: 177 Copynumber: 3.6 Consensus size: 176
2657 GAATGTTCGG
* * * * ** *
2667 GGTCAAAAATGGAATTTT-CAAACATTCGAGGATAAAATGGTAATTTTTTGAAAGTTTAGGGTTT
1 GGTCAAAAATAGAATTTTGGAAA-GTTCGAGGGTAAAATGGTAATTTTTAAAAAG-TTAGGGTTA
* * * * * * * *
2731 AAAATGGAATTTTTAGACA-TTCGGGGGTAAAATAGTAATTTTAGG-AAAATTGTGG-TCAAAAT
64 AAAATGGAA-TTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAAT
* * * * **
2793 GGAATTTTAGG-AATTTCGAGGGTAAATTGGTAACTTTTGGAAAAATCGA
128 GGAATTTT-GGAAAGTTAGAGGGTAAAATGGTAATTTTTGGAAAAATAAA
* * * * * * *
2842 GGTC-AAAATGGAATTTTTGG-GAGTTCTAGGGTAAAACGATAATTTTTAGAAAAATCAGGGTTA
1 GGTCAAAAATAGAA-TTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTA-AAAAGTTAGGGTTA
* *
2905 AAAATGAAATTTTGGAAAGTTCGAGGGTAAAGTGGTAATTTTTGGAAAAATCGAGGTTAAAAATG
64 AAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAATG
*
2970 GAATTTTGGAAAGTTAGAGGGTAAAATGGTAATTTTTTAGAAAAATAAA
129 GAATTTTGGAAAGTTAGAGGGTAAAATGGTAA-TTTTTGGAAAAATAAA
* * **
3019 GGCCAAAAATAGAATTTTGGAAAGTTCGAGGGTAAATTGGTAATTTTTTTTAAA-TTAGGGTTAA
1 GGTCAAAAATAGAATTTTGGAAAGTTCGAGGGTAAAATGGTAA-TTTTTAAAAAGTTAGGGTTAA
** * * * * * *
3083 AAATGGAATCATGGAAAGTT-TAGGGTTAAAATGGTAATTTTTGCAAAAATCAAGATCAAAAATA
65 AAATGGAATTTTGGAAAGTTCGAGGG-TAAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAATG
* *
3147 GAATTTTGGAAAGTTCAG-GGGTAAAATGGTAATTTTTGGAAAAAATTAG
129 GAATTTTGGAAAGTT-AGAGGGTAAAATGGTAATTTTTGG-AAAAATAAA
3196 GGTCAAAAATAGAATTTTGGAAAGTTCGAGGGTAAAAAT-GTAATTTTTAAAAAGTTTAGGGTTA
1 GGTCAAAAATAGAATTTTGGAAAGTTCGAGGGT-AAAATGGTAATTTTTAAAAAG-TTAGGGTTA
* ** *
3260 AAAATGGCATTTTGGAAAAGTTTAAGGGTCAAAAT-ATAATTTTTGGA
64 AAAATGGAATTTTGG-AAAGTTCGAGGGT-AAAATGGTAATTTTTGGA
3307 CAAGTTAGGG
Statistics
Matches: 383, Mismatches: 62, Indels: 36
0.80 0.13 0.07
Matches are distributed among these distances:
173 7 0.02
174 66 0.17
175 22 0.06
176 51 0.13
177 151 0.39
178 55 0.14
179 22 0.06
180 9 0.02
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.33
Consensus pattern (176 bp):
GGTCAAAAATAGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTAAAAAGTTAGGGTTAAA
AATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAATGGA
ATTTTGGAAAGTTAGAGGGTAAAATGGTAATTTTTGGAAAAATAAA
Found at i:3280 original size:60 final size:58
Alignment explanation
Indices: 2666--3303 Score: 476
Period size: 59 Copynumber: 10.8 Consensus size: 58
2656 GGAATGTTCG
* * * * * **
2666 GGGTCAAAAATGGAATTTT-CAAACATTCGAGGATAAAATGGTAATTTTTTGAAAGTTTA
1 GGGTTAAAAATGGAATTTTGGAAA-GTTCGAGGGTAAAATGGTAA-TTTTTAAAAAATTA
* * * * * *
2725 GGGTTTAAAATGGAATTTTTAGACA-TTCGGGGGTAAAATAGTAA-TTTTAGGAAAATT-
1 GGGTTAAAAATGGAA-TTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTA-AAAAATTA
* * * ** *
2782 GTGG-TCAAAATGGAATTTTAGG-AATTTCGAGGGTAAATTGGTAACTTTTGGAAAAA-TC
1 G-GGTTAAAAATGGAATTTT-GGAAAGTTCGAGGGTAAAATGGTAA-TTTTTAAAAAATTA
* * * * * *
2840 GAGG-TCAAAATGGAATTTTTGG-GAGTTCTAGGGTAAAACGATAATTTTTAGAAAAATCA
1 G-GGTTAAAAATGGAA-TTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTA-AAAAATTA
* * * *
2899 GGGTTAAAAATGAAATTTTGGAAAGTTCGAGGGTAAAGTGGTAATTTTTGGAAAAA-TC
1 GGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTT-AAAAAATTA
* *
2957 GAGGTTAAAAATGGAATTTTGGAAAGTTAGAGGGTAAAATGGTAATTTTTTAGAAAAATAA
1 G-GGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAA-TTTTTA-AAAAATTA
* ** * * ***
3018 AGGCCAAAAATAGAATTTTGGAAAGTTCGAGGGTAAATTGGTAATTTTTTTTAAATTA
1 GGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTAAAAAATTA
** * * *
3076 GGGTTAAAAATGGAATCATGGAAAGTT-TAGGGTTAAAATGGTAATTTTTGCAAAAATCA
1 GGGTTAAAAATGGAATTTTGGAAAGTTCGAGGG-TAAAATGGTAATTTTT-AAAAAATTA
* * * *
3135 AGATCAAAAATAGAATTTTGGAAAGTTC-AGGGGTAAAATGGTAATTTTTGGAAAAAATTA
1 GGGTTAAAAATGGAATTTTGGAAAGTTCGA-GGGTAAAATGGTAATTTTT--AAAAAATTA
* * *
3195 GGGTCAAAAATAGAATTTTGGAAAGTTCGAGGGTAAAAAT-GTAATTTTTAAAAAGTTTA
1 GGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGT-AAAATGGTAATTTTTAAAAA-ATTA
* ** *
3254 GGGTTAAAAATGGCATTTTGGAAAAGTTTAAGGGTCAAAAT-ATAATTTTT
1 GGGTTAAAAATGGAATTTTGG-AAAGTTCGAGGGT-AAAATGGTAATTTTT
3304 GGACAAGTTA
Statistics
Matches: 464, Mismatches: 87, Indels: 55
0.77 0.14 0.09
Matches are distributed among these distances:
56 5 0.01
57 41 0.09
58 102 0.22
59 182 0.39
60 126 0.27
61 8 0.02
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.33
Consensus pattern (58 bp):
GGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTAAAAAATTA
Found at i:3312 original size:31 final size:30
Alignment explanation
Indices: 3097--3316 Score: 109
Period size: 30 Copynumber: 7.4 Consensus size: 30
3087 GGAATCATGG
* * *
3097 AAAGTTTAGGGTTAAAATGGTAATTTTTGCA
1 AAAGTTTAGGGTCAAAAT-ATAATTTTTGGA
* * * * *
3128 AAA-ATCAAGATCAAAA-ATAGAATTTTGG-
1 AAAGTTTAGGGTCAAAATATA-ATTTTTGGA
* *
3156 AAAGTTCAGGGGT-AAAATGGTAATTTTTGGA
1 AAAGTTTA-GGGTCAAAAT-ATAATTTTTGGA
** *
3187 AAAAATTAGGGTCAAAA-ATAGAATTTTGG-
1 AAAGTTTAGGGTCAAAATATA-ATTTTTGGA
* * * *
3216 AAAGTTCGAGGGTAAAAATGTAATTTTT-AA
1 AAAGTT-TAGGGTCAAAATATAATTTTTGGA
* *
3246 AAAGTTTAGGGTTAAAA-ATGGCA-TTTTGGA
1 AAAGTTTAGGGTCAAAATAT--AATTTTTGGA
3276 AAAGTTTAAGGGTCAAAATATAATTTTTGGA
1 AAAGTTT-AGGGTCAAAATATAATTTTTGGA
*
3307 CAAG-TTAGGG
1 AAAGTTTAGGG
3317 ACCTTCAGGA
Statistics
Matches: 139, Mismatches: 33, Indels: 36
0.67 0.16 0.17
Matches are distributed among these distances:
28 6 0.04
29 36 0.26
30 60 0.43
31 35 0.25
32 2 0.01
ACGTcount: A:0.41, C:0.04, G:0.23, T:0.32
Consensus pattern (30 bp):
AAAGTTTAGGGTCAAAATATAATTTTTGGA
Found at i:4329 original size:3 final size:3
Alignment explanation
Indices: 4313--4378 Score: 60
Period size: 3 Copynumber: 21.3 Consensus size: 3
4303 TTCAACTTTG
* * * * *
4313 ATT ATT AAT GTT ATT ATCA ATT ATT ATT AATT AAT ATT ATT GTT ATT
1 ATT ATT ATT ATT ATT AT-T ATT ATT ATT -ATT ATT ATT ATT ATT ATT
*
4360 ATT ATT AAT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT A
4379 CTGATTCATT
Statistics
Matches: 49, Mismatches: 12, Indels: 4
0.75 0.18 0.06
Matches are distributed among these distances:
3 44 0.90
4 5 0.10
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:5706 original size:49 final size:49
Alignment explanation
Indices: 5582--6077 Score: 383
Period size: 49 Copynumber: 10.1 Consensus size: 49
5572 TGTTTTCATT
* * * *
5582 GTACCGGATTCGCCATTGCGGCTTAAATCTTTCTCTTTCATG-CTTC-TG
1 GTACTGGATTCGCCATTGCGACTTAAACCTTTC-CCTTCATGTCTTCGTG
* * *
5630 AGTTA-TAAGG-TTCGCCATTGTGACTTAAGCCTTTCCCTTCGTGTCTTCGTG
1 -G-TACT--GGATTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTTCGTG
* * * * * *
5681 GTACTGGATTCGCCTTTGCGGCTTAAATCTTTCCCTTTACG-CTTCTGAG
1 GTACTGGATTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTTC-GTG
* ** *
5730 GTACAAGG-TTTACCATTGTGACTTAAACCTTTCTCC-TCATGTCTTCGTG
1 GTAC-TGGATTCGCCATTGCGACTTAAACCTTTC-CCTTCATGTCTTCGTG
* * * *
5779 GTACTGGATTCTCCGTTGCGGCTTAAATCC-TTCCCTTCATGT-TTCTGAG
1 GTACTGGATTCGCCATTGCGACTTAAA-CCTTTCCCTTCATGTCTTC-GTG
**
5828 GTACTAGG-TTCGCCATTGCGACTTAAACCTTTCCCTTTTTGTCTTCGTG
1 GTACT-GGATTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTTCGTG
* ** * *
5877 GTACTGGATTCACCGCTGCGGCTTAAATCC-TTCCCTTCATGTC-TCTGAG
1 GTACTGGATTCGCCATTGCGACTTAAA-CCTTTCCCTTCATGTCTTC-GTG
** * *
5926 GTACTAGG-TTCATCATTGCGACTTAAACCTTTCCCTTTATG-CTTCTGAG
1 GTACT-GGATTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTTC-GTG
** * * * * *
5975 GTACACGATTCGCCGTTGTGACTTAAACCTTTCCCTCCATATCTTCATG
1 GTACTGGATTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTTCGTG
**
6024 GTACTGGATTCGCCATTGCGACTTAAATTTTTCCCTTCATGT-TTCGTG
1 GTACTGGATTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTTCGTG
6072 GTACTG
1 GTACTG
6078 AGACCTATAG
Statistics
Matches: 350, Mismatches: 71, Indels: 53
0.74 0.15 0.11
Matches are distributed among these distances:
48 34 0.10
49 260 0.74
50 52 0.15
51 4 0.01
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.38
Consensus pattern (49 bp):
GTACTGGATTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTTCGTG
Found at i:5773 original size:98 final size:98
Alignment explanation
Indices: 5582--6077 Score: 529
Period size: 98 Copynumber: 5.1 Consensus size: 98
5572 TGTTTTCATT
* * * * * *
5582 GTACCGGATTCGCCATTGCGGCTTAAATCTTTCTCTTTCATGCTTCTGAGTTATAAGGTTCGCCA
1 GTACTGGATTCGCCGTTGCGGCTTAAATCTTTC-CCTTCATGCTTCTGAGGTACAAGGTTCACCA
* * *
5647 TTGTGACTTAAGCCTTTCCCTTCGTGTCTTCGTG
65 TTGCGACTTAAACCTTTCCCTTCATGTCTTCGTG
* * * *
5681 GTACTGGATTCGCCTTTGCGGCTTAAATCTTTCCCTTTACGCTTCTGAGGTACAAGGTTTACCAT
1 GTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCACCAT
*
5746 TGTGACTTAAACCTTTCTCC-TCATGTCTTCGTG
66 TGCGACTTAAACCTTTC-CCTTCATGTCTTCGTG
* * * * *
5779 GTACTGGATTCTCCGTTGCGGCTTAAATCCTTCCCTTCATGTTTCTGAGGTACTAGGTTCGCCAT
1 GTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCACCAT
**
5844 TGCGACTTAAACCTTTCCCTTTTTGTCTTCGTG
66 TGCGACTTAAACCTTTCCCTTCATGTCTTCGTG
* * * * *
5877 GTACTGGATTCACCGCTGCGGCTTAAATCCTTCCCTTCATG-TCTCTGAGGTACTAGGTTCATCA
1 GTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCT-TCTGAGGTACAAGGTTCACCA
* *
5941 TTGCGACTTAAACCTTTCCCTTTATG-CTTCTGAG
65 TTGCGACTTAAACCTTTCCCTTCATGTCTTC-GTG
** * * * * * * *
5975 GTACACGATTCGCCGTTGTGACTTAAACCTTTCCCTCCATATCTTC--ATGGTAC-TGGATTCGC
1 GTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCAT-GCTTCTGA-GGTACAAGG-TTCAC
**
6037 CATTGCGACTTAAATTTTTCCCTTCATGT-TTCGTG
63 CATTGCGACTTAAACCTTTCCCTTCATGTCTTCGTG
6072 GTACTG
1 GTACTG
6078 AGACCTATAG
Statistics
Matches: 340, Mismatches: 48, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
97 16 0.05
98 288 0.85
99 35 0.10
100 1 0.00
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.38
Consensus pattern (98 bp):
GTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCACCAT
TGCGACTTAAACCTTTCCCTTCATGTCTTCGTG
Found at i:15958 original size:13 final size:13
Alignment explanation
Indices: 15942--15967 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15932 GCTGTCATGG
15942 TTAGAATTCTATT
1 TTAGAATTCTATT
15955 TTAGAATTCTATT
1 TTAGAATTCTATT
15968 AGGGTTAGGA
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:0.08, G:0.08, T:0.54
Consensus pattern (13 bp):
TTAGAATTCTATT
Found at i:23953 original size:22 final size:21
Alignment explanation
Indices: 23927--23967 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
23917 TTGATTATGA
23927 AAATGATTAATTAAGGTTAATT
1 AAATGATTAATTAA-GTTAATT
* *
23949 AAATGGTTTATTAAGTTAA
1 AAATGATTAATTAAGTTAA
23968 CCATAAAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (21 bp):
AAATGATTAATTAAGTTAATT
Found at i:24934 original size:51 final size:51
Alignment explanation
Indices: 24857--25068 Score: 237
Period size: 51 Copynumber: 4.1 Consensus size: 51
24847 CTAAGAGTCA
* * *
24857 TGAGTAAATGAATCCTTTATGAATTAAAGGTTCGATGACTAAGTGTCATCG
1 TGAGTAAATAAATCCTTTATGGATTAAAGGTCCGATGACTAAGTGTCATCG
* * * *
24908 TGAGTAAATAAATCCTTTACGGATTAAATGTCCAATAACTAAGTGTCATCG
1 TGAGTAAATAAATCCTTTATGGATTAAAGGTCCGATGACTAAGTGTCATCG
* * * * *
24959 TGAATAAATGAATCCATGATGGATTAAAGGTCCGATGACTCAGTGTCATCG
1 TGAGTAAATAAATCCTTTATGGATTAAAGGTCCGATGACTAAGTGTCATCG
* * * **
25010 TGAGTATATGAATTCCTATATGGAACAAGAGGTCCGATGACTATA-TGTCATCG
1 TGAGTAAAT-AAATCCTTTATGGATTAA-AGGTCCGATGACTA-AGTGTCATCG
25063 TGAGTA
1 TGAGTA
25069 TTAAATGAAA
Statistics
Matches: 132, Mismatches: 26, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
51 93 0.70
52 11 0.08
53 27 0.20
54 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (51 bp):
TGAGTAAATAAATCCTTTATGGATTAAAGGTCCGATGACTAAGTGTCATCG
Found at i:25060 original size:53 final size:52
Alignment explanation
Indices: 24951--25128 Score: 150
Period size: 60 Copynumber: 3.3 Consensus size: 52
24941 AATAACTAAG
* * ** *
24951 TGTCATCGTGAATAAATGAA-TCCATGATGGATTAA-AGGTCCGATGACTCA-G
1 TGTCATCGTGAGTATATGAATTCCAT-ATGGAACAAGAGGTCCGATGACT-ATA
25002 TGTCATCGTGAGTATATGAATTCCTATATGGAACAAGAGGTCCGATGACTATA
1 TGTCATCGTGAGTATATGAATTCC-ATATGGAACAAGAGGTCCGATGACTATA
*
25055 TGTCATCGTGAGTATTAAATGAAATGAGTTCCA-ATGCGGAACAAG-GGTCCGATGACTTTA
1 TGTCATCGTGAGTA-T--ATG--A--A-TTCCATAT--GGAACAAGAGGTCCGATGACTATA
25115 TGTCATCGTGAGTA
1 TGTCATCGTGAGTA
25129 ACAAATGCGA
Statistics
Matches: 107, Mismatches: 6, Indels: 19
0.81 0.05 0.14
Matches are distributed among these distances:
51 18 0.17
52 11 0.10
53 29 0.27
54 1 0.01
56 3 0.03
58 1 0.01
59 2 0.02
60 30 0.28
61 12 0.11
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.29
Consensus pattern (52 bp):
TGTCATCGTGAGTATATGAATTCCATATGGAACAAGAGGTCCGATGACTATA
Done.