Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold967
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: 3776
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.29
Warning! 285 characters in sequence are not A, C, G, or T
Found at i:426 original size:18 final size:18
Alignment explanation
Indices: 405--442 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
395 CAAAAGGAAG
405 GAAAATAAAGAAAGAAAA
1 GAAAATAAAGAAAGAAAA
* *
423 GAAAATAAATAAATAAAA
1 GAAAATAAAGAAAGAAAA
441 GA
1 GA
443 GGAATAGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (18 bp):
GAAAATAAAGAAAGAAAA
Found at i:846 original size:18 final size:18
Alignment explanation
Indices: 804--846 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
794 AATTGGGCCT
*
804 TTAGGTTTTTTTATATTA
1 TTAGGTTTTGTTATATTA
* * *
822 TTGGGTTTTGTTATTTTG
1 TTAGGTTTTGTTATATTA
840 TTAGGTT
1 TTAGGTT
847 ATTTGGGTAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.14, C:0.00, G:0.21, T:0.65
Consensus pattern (18 bp):
TTAGGTTTTGTTATATTA
Found at i:1221 original size:50 final size:50
Alignment explanation
Indices: 1141--2487 Score: 1140
Period size: 50 Copynumber: 27.1 Consensus size: 50
1131 ATTCTATTCC
** * *
1141 ACTGCAATGTCAGGGGGGTAAGATCTGCTGTTGTAGCTTCAATCTTTTTA
1 ACTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCA
* * *
1191 ATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCC
1 ACTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCA
** * *
1241 ACTGCAA-CACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTA
1 ACTGCAATGTC-AGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCA
* ** * * *
1291 ACTGC-----CGGGGAAACAAAATCCACTGTTGTAGCTTCAAT-TTGTTCC
1 ACTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTT-TTCA
* ** * * *
1336 GCTGCAA-CACTAGGAAAGTAAGATCCACTGTTGTAGCTTCAATCTTTTTA
1 ACTGCAATGTC-AGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCA
* ** * *
1386 ACTGC-----CGGGGAAACAAGATCCGCTGTTGTAGCTTCAATCTGTTCC
1 ACTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCA
** * *
1431 ACTGCAA-CACTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTA
1 ACTGCAATGTC-AGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCA
* * * *
1481 ATTGCAATGTCAGGGAAGTAAGATCCACTGTTGTAGCTTCAATCTATTCC
1 ACTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCA
* * * * * * * *
1531 ACTGCAACG-CTAGGAAAGTAAGATTCACCGTCGTGGCCTCAATC-TTTCA
1 ACTGCAATGTC-AGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCA
* * ** * * ** ** * *
1580 ATTGCAATATCAGAAAAAATGAGATTTGCCATTGTAGCTTCAATCTATTCT
1 ACTGCAATGTCAG-GGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCA
* ** * * * * ** * *
1631 GCTATACTGCCTGGGAAGTAAGATTCGCCATTGTGGCTTCAATCTTTTGA
1 ACTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCA
** ** * ** * * *
1681 GTTGCAATGTTGGGGAAGTAAGATTCGCCATTGTGGCTTCAATCTGTTCC
1 ACTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCA
* * * * * * *
1731 GCTGCATTGCCTGGGAAATAAGATCCGCTGTTGTAGCTTTAATCTTTTTA
1 ACTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCA
* * * *** *
1781 ATTACAATGTCAGGGAAGTAAGATCCACTGTTGTAGCTTCAATCCACTCC
1 ACTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCA
* * *
1831 ACTGCAACG-CTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTA
1 ACTGCAATGTC-AGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCA
* * * *
1881 ATTGCAATGTCAGTGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCC
1 ACTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCA
* ** * *
1931 ACTGCAACG-CTAGAAAAGTAAGATCCGCTATTGTAGCTTCAATCTTTTTA
1 ACTGCAATGTC-AGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCA
* * *
1981 ATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCC
1 ACTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCA
* * * *
2031 ACTGTAACG-CTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTA
1 ACTGCAATGTC-AGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCA
* * ** * *
2081 ATTGCAATGTCAGCGAAGTAAGATCCATTGTTGTAGCTTCAATCTGTTCC
1 ACTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCA
* *
2131 ACTGCAATG-CTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTA
1 ACTGCAATGTC-AGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCA
* * * * *
2181 ATTGCAATGTCAGGGAAGTAAGATCCGCGGTTGTAGCTTCAACCTATTCC
1 ACTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCA
* * * *
2231 ACTGTAATG-CTAGGAAAGTAAGATCCGCTGTTATAGCTTCAATCTTTTTA
1 ACTGCAATGTC-AGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCA
* * *
2281 ATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCC
1 ACTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCA
* *
2331 ACTGCAATG-CTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTA
1 ACTGCAATGTC-AGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCA
* * *
2381 ATTGCAATGTCCGGGAAGTAAGATCCGCTGTTGTAGCTTCAAT-TTGTTCC
1 ACTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTT-TTCA
** * *
2431 ACTATAATG-CTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTA
1 ACTGCAATGTC-AGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCA
*
2481 ATTGCAA
1 ACTGCAA
2488 ACTATGGTTT
Statistics
Matches: 1030, Mismatches: 234, Indels: 66
0.77 0.18 0.05
Matches are distributed among these distances:
44 2 0.00
45 68 0.07
46 2 0.00
49 24 0.02
50 915 0.89
51 19 0.02
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (50 bp):
ACTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTCA
Found at i:1271 original size:100 final size:100
Alignment explanation
Indices: 1158--2487 Score: 1783
Period size: 100 Copynumber: 13.4 Consensus size: 100
1148 TGTCAGGGGG
*
1158 GTAAGATCTGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTT
1 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTT
*
1223 GTAGCTTCAATCTGTTCCACTGCAACACTAGGAAA
66 GTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAA
* * ** * *
1258 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAA---C--TGCCGGGGAAACAAAATCCACTGTT
1 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTT
* * *
1318 GTAGCTTCAATTTGTTCCGCTGCAACACTAGGAAA
66 GTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAA
* * * **
1353 GTAAGATCCACTGTTGTAGCTTCAATCTTTTTAA---C--TGCCGGGGAAACAAGATCCGCTGTT
1 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTT
*
1413 GTAGCTTCAATCTGTTCCACTGCAACACTAGGAAA
66 GTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAA
*
1448 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATCCACTGTT
1 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTT
*
1513 GTAGCTTCAATCTATTCCACTGCAACGCTAGGAAA
66 GTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAA
* * * * * * * * ** * * ** **
1548 GTAAGATTCACCGTCGTGGCCTCAATC-TTTCAATTGCAATATCAGAAAAAATGAGATTTGCCAT
1 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAG-GGAAGTAAGATCCGCTGT
* *
1612 TGTAGCTTCAATCTATT---CTGCTATACTGCCT-GGGAA
65 TGTAGCTTCAATCTGTTCCACTGC-A-AC-G-CTAGGAAA
* ** * * * ** * **
1648 GTAAGATTCGCCATTGTGGCTTCAATCTTTTGAGTTGCAATGTTGGGGAAGTAAGATTCGCCATT
1 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTT
* * ** *
1713 GTGGCTTCAATCTGTTCCGCTGCATTGCCTGGGAAA
66 GTAGCTTCAATCTGTTCCACTGCAACG-CTAGGAAA
* * *
1749 -TAAGATCCGCTGTTGTAGCTTTAATCTTTTTAATTACAATGTCAGGGAAGTAAGATCCACTGTT
1 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTT
***
1813 GTAGCTTCAATCCACTCCACTGCAACGCTAGGAAA
66 GTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAA
*
1848 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGTGAAGTAAGATCCGCTGTT
1 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTT
*
1913 GTAGCTTCAATCTGTTCCACTGCAACGCTAGAAAA
66 GTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAA
*
1948 GTAAGATCCGCTATTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTT
1 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTT
*
2013 GTAGCTTCAATCTGTTCCACTGTAACGCTAGGAAA
66 GTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAA
* **
2048 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGCGAAGTAAGATCCATTGTT
1 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTT
*
2113 GTAGCTTCAATCTGTTCCACTGCAATGCTAGGAAA
66 GTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAA
*
2148 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCGGTT
1 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTT
* * * *
2213 GTAGCTTCAACCTATTCCACTGTAATGCTAGGAAA
66 GTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAA
*
2248 GTAAGATCCGCTGTTATAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTT
1 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTT
*
2313 GTAGCTTCAATCTGTTCCACTGCAATGCTAGGAAA
66 GTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAA
*
2348 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCCGGGAAGTAAGATCCGCTGTT
1 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTT
* ** *
2413 GTAGCTTCAATTTGTTCCACTATAATGCTAGGAAA
66 GTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAA
2448 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAA
1 GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAA
2488 ACTATGGTTT
Statistics
Matches: 1098, Mismatches: 116, Indels: 32
0.88 0.09 0.03
Matches are distributed among these distances:
95 175 0.16
97 5 0.00
98 2 0.00
99 25 0.02
100 867 0.79
101 19 0.02
102 1 0.00
103 4 0.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (100 bp):
GTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTT
GTAGCTTCAATCTGTTCCACTGCAACGCTAGGAAA
Found at i:2664 original size:86 final size:87
Alignment explanation
Indices: 2522--2684 Score: 247
Period size: 86 Copynumber: 1.9 Consensus size: 87
2512 GCTTGCAGTA
* * * * * *
2522 CAGGAAGGCAAGATCTGTTATCTTTACCCAGTTCCACTGCAACCGATGAAGGCAAGGTTTTGTTT
1 CAGGAAGGCAAAATCTGCTATCTTTAACCAGCTCCACAGCAACCAATGAAGGCAAGGTTTTGTTT
*
2587 TCAATCTGCTTCGTTGTTAATG
66 TCAATCTACTTCGTTGTTAATG
2609 CAGGAAGGCAAAATCTGCT-TCTTTAACCAGCTCCACAGCAACCAATGAAGGCAAGGTTTTGTTT
1 CAGGAAGGCAAAATCTGCTATCTTTAACCAGCTCCACAGCAACCAATGAAGGCAAGGTTTTGTTT
*
2673 TCGATCTACTTC
66 TCAATCTACTTC
2685 TTTAACCAGC
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
86 51 0.75
87 17 0.25
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (87 bp):
CAGGAAGGCAAAATCTGCTATCTTTAACCAGCTCCACAGCAACCAATGAAGGCAAGGTTTTGTTT
TCAATCTACTTCGTTGTTAATG
Found at i:2710 original size:55 final size:56
Alignment explanation
Indices: 2621--2740 Score: 215
Period size: 55 Copynumber: 2.2 Consensus size: 56
2611 GGAAGGCAAA
2621 ATCTGCTTCTTTAACCAGCTCCACAGCAACCAATGAAGGCAAGG-TTTTGTTTTCG
1 ATCTGCTTCTTTAACCAGCTCCACAGCAACCAATGAAGGCAAGGCTTTTGTTTTCG
* *
2676 ATCTACTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTTTGTTTTCG
1 ATCTGCTTCTTTAACCAGCTCCACAGCAACCAATGAAGGCAAGGCTTTTGTTTTCG
2732 ATCTGCTTC
1 ATCTGCTTC
2741 ACTGTTAATG
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
55 42 0.69
56 19 0.31
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.33
Consensus pattern (56 bp):
ATCTGCTTCTTTAACCAGCTCCACAGCAACCAATGAAGGCAAGGCTTTTGTTTTCG
Found at i:2792 original size:142 final size:141
Alignment explanation
Indices: 2542--2826 Score: 446
Period size: 142 Copynumber: 2.0 Consensus size: 141
2532 AGATCTGTTA
* * * **
2542 TCTTTACCCAGTTCCACTGCAACCGATGAAGGCAAGGTTTTGTTTTCAATCTGCTTCGTTGTTAA
1 TCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGTTTTGTTTTCAATCTGCTTCACTGTTAA
* *
2607 TGCAGGAAGGCAAAATCTGCTTCTTTAACCAGCTCCACAGCAACCAATGAAGGCAAGG-TTTTGT
66 TGCAGGAAGACAAAATCTGCTTCTTTAACCAGCTCCACAGCAACCAATGAAGGAAAGGCTTTT-T
2671 TTTCGATCTACT
130 TTTCGATCTACT
*
2683 TCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTTTGTTTTCGATCTGCTTCACTGTTA
1 TCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGG-TTTTGTTTTCAATCTGCTTCACTGTTA
* *
2748 ATGCAGGAAGACAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGAAAGGCTTTTT
65 ATGCAGGAAGACAAAATCTGCTTCTTTAACCAGCTCCACAGCAACCAATGAAGGAAAGGCTTTTT
*
2813 TTTCGATCTGCT
130 TTTCGATCTACT
2825 TC
1 TC
2827 GCTGTTAATG
Statistics
Matches: 131, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
141 34 0.26
142 93 0.71
143 4 0.03
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.32
Consensus pattern (141 bp):
TCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGTTTTGTTTTCAATCTGCTTCACTGTTAA
TGCAGGAAGACAAAATCTGCTTCTTTAACCAGCTCCACAGCAACCAATGAAGGAAAGGCTTTTTT
TTCGATCTACT
Found at i:2857 original size:86 final size:86
Alignment explanation
Indices: 2675--3124 Score: 686
Period size: 86 Copynumber: 5.2 Consensus size: 86
2665 TTTTGTTTTC
* * *
2675 GATCTACTTCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTTTGTTTTCGATCTGCTT
1 GATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTT-TTTTCGATCTGCTT
** *
2740 CACTGTTAATGCAGGAAGACAA
65 CACTGTTAACACAGGAAGGCAA
* * *
2762 GATCTGCTTCTTTAACCAGCTCCACTGCAACCAATGAAGGAAAGGCTTTTTTTTCGATCTGCTTC
1 GATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTTTTTTCGATCTGCTTC
* ** *
2827 GCTGTTAATGCAGGAAGGTAA
66 ACTGTTAACACAGGAAGGCAA
* *
2848 GATCTGCTTCTTTAACCAGCTCCATTGCCACCGATGGAGGCAAGG-TTTTGTTTTCGATCTGCTT
1 GATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTT-TTTTCGATCTGCTT
* *
2912 CACTTTTAAAACAGGAAGGCAA
65 CACTGTTAACACAGGAAGGCAA
*
2934 GATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTC
1 GATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTTTTTTCGATCTGCTTC
*
2999 TCTGTTAACACAGGAAGGCAA
66 ACTGTTAACACAGGAAGGCAA
*
3020 GATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGCTTC
1 GATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTTTTTTCGATCTGCTTC
*
3085 TCTGTTAACACAGGAAGGCAA
66 ACTGTTAACACAGGAAGGCAA
3106 GATCTGCTTCTTTAACCAG
1 GATCTGCTTCTTTAACCAG
3125 NNNNNNNNNN
Statistics
Matches: 340, Mismatches: 21, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
85 4 0.01
86 285 0.84
87 51 0.15
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (86 bp):
GATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTTTTTTCGATCTGCTTC
ACTGTTAACACAGGAAGGCAA
Found at i:2975 original size:43 final size:43
Alignment explanation
Indices: 2928--3063 Score: 127
Period size: 43 Copynumber: 3.2 Consensus size: 43
2918 TAAAACAGGA
2928 AGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGG
1 AGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGG
* * ** * * * * *
2971 AGGCAAGGCTTTG-TT-TTCGATCTGCTTCTCTGTTAACAC-A-GG
1 AGGCAA-GATCTGCTTCTTTAACCAGCTCCACTG-CAAC-CGATGG
3013 AAGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGG
1 -AGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGG
3057 AGGCAAG
1 AGGCAAG
3064 GCTTTGTTTT
Statistics
Matches: 67, Mismatches: 18, Indels: 16
0.66 0.18 0.16
Matches are distributed among these distances:
42 18 0.27
43 31 0.46
44 18 0.27
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (43 bp):
AGGCAAGATCTGCTTCTTTAACCAGCTCCACTGCAACCGATGG
Found at i:3104 original size:43 final size:43
Alignment explanation
Indices: 2971--3106 Score: 127
Period size: 43 Copynumber: 3.2 Consensus size: 43
2961 CAACCGATGG
2971 AGGCAAGGCTTTGTTTTCGATCTGCTTCTCTGTTAACACAGGA
1 AGGCAAGGCTTTGTTTTCGATCTGCTTCTCTGTTAACACAGGA
* * ** * * * * *
3014 AGGCAA-GATCTGCTTCTTTAACCAGCTCCACTG-CAAC-CGATGG-
1 AGGCAAGGCTTTG-TT-TTCGATCTGCTTCTCTGTTAACAC-A-GGA
3057 AGGCAAGGCTTTGTTTTCGATCTGCTTCTCTGTTAACACAGGA
1 AGGCAAGGCTTTGTTTTCGATCTGCTTCTCTGTTAACACAGGA
3100 AGGCAAG
1 AGGCAAG
3107 ATCTGCTTCT
Statistics
Matches: 67, Mismatches: 18, Indels: 16
0.66 0.18 0.16
Matches are distributed among these distances:
42 18 0.27
43 31 0.46
44 18 0.27
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (43 bp):
AGGCAAGGCTTTGTTTTCGATCTGCTTCTCTGTTAACACAGGA
Found at i:3510 original size:45 final size:44
Alignment explanation
Indices: 3373--3512 Score: 119
Period size: 44 Copynumber: 3.2 Consensus size: 44
3363 NNNNNCAGGA
*
3373 AGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAG
1 AGGCAAGATCGTTTGTCTTCAACCAGCTCCATCACAACCGAGAG
* ** * ** *
3417 AGGCAAG---GTTTGTATCTTCGACTTGCTTCACTGTCAA-TGCAG-G
1 AGGCAAGATCGTTTG--TCTTCAACCAGCTCCA-TCACAACCG-AGAG
3460 AAGGCAAGATCGTTTGTCTTCAACCAGCTCCATCACAACCGAAGAG
1 -AGGCAAGATCGTTTGTCTTCAACCAGCTCCATCACAACCG-AGAG
3506 AGGCAAG
1 AGGCAAG
3513 TTTGTGTCTA
Statistics
Matches: 70, Mismatches: 16, Indels: 19
0.67 0.15 0.18
Matches are distributed among these distances:
41 4 0.06
43 14 0.20
44 24 0.34
45 22 0.31
46 1 0.01
47 5 0.07
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.24
Consensus pattern (44 bp):
AGGCAAGATCGTTTGTCTTCAACCAGCTCCATCACAACCGAGAG
Done.