Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3186.1
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: 153920
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.30
Warning! 7092 characters in sequence are not A, C, G, or T
Found at i:1865 original size:41 final size:43
Alignment explanation
Indices: 1776--1869 Score: 104
Period size: 41 Copynumber: 2.2 Consensus size: 43
1766 GTCTTAGATG
* * *
1776 TGGTCTTACATGCTATCACATATCGATGCCACTGTCCCAGACA
1 TGGTCTTACATGCAATCAAATATCGATGCCACTGTCCCAAACA
* * *
1819 GGGTCTTACATG-AATCAAATA-CGATGTCGA-TGTCCTAAACA
1 TGGTCTTACATGCAATCAAATATCGATG-CCACTGTCCCAAACA
1860 TGGTCTTACA
1 TGGTCTTACA
1870 CGTAACCACA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
41 23 0.53
42 9 0.21
43 11 0.26
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (43 bp):
TGGTCTTACATGCAATCAAATATCGATGCCACTGTCCCAAACA
Found at i:3857 original size:43 final size:42
Alignment explanation
Indices: 3779--3874 Score: 95
Period size: 43 Copynumber: 2.3 Consensus size: 42
3769 AGCATATACA
* * * *
3779 ATGCCAAC-GTCCCGGACATGGTCTTACATGTAATCAAACATCG
1 ATGCC-ACTGTCCCAGACAGGGTCTTACACGAAATCAAACA-CG
* * *
3822 ATGCCACTGTCCCAGACAGGGTCTTATACGAAATCAGATACG
1 ATGCCACTGTCCCAGACAGGGTCTTACACGAAATCAAACACG
*
3864 ATGCCAATGTC
1 ATGCCACTGTC
3875 TTAAACATGG
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
42 14 0.32
43 30 0.68
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (42 bp):
ATGCCACTGTCCCAGACAGGGTCTTACACGAAATCAAACACG
Found at i:10268 original size:34 final size:34
Alignment explanation
Indices: 10225--10297 Score: 137
Period size: 34 Copynumber: 2.1 Consensus size: 34
10215 AAGATATATT
10225 GTTTTAAAATTAATAATAAATTTAATATGGTTAA
1 GTTTTAAAATTAATAATAAATTTAATATGGTTAA
10259 GTTTTAAAATTAATAATAAATTTAATATGGTTAA
1 GTTTTAAAATTAATAATAAATTTAATATGGTTAA
*
10293 CTTTT
1 GTTTT
10298 TGTCAAATGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.44, C:0.01, G:0.08, T:0.47
Consensus pattern (34 bp):
GTTTTAAAATTAATAATAAATTTAATATGGTTAA
Found at i:26097 original size:24 final size:24
Alignment explanation
Indices: 26069--26117 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
26059 TTGTTAACTT
26069 AGTTAATAATTAGATTTTCAATTA
1 AGTTAATAATTAGATTTTCAATTA
26093 AGTTAATAATTAGATTTTCAATTA
1 AGTTAATAATTAGATTTTCAATTA
26117 A
1 A
26118 TTCTAGGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (24 bp):
AGTTAATAATTAGATTTTCAATTA
Found at i:27889 original size:390 final size:387
Alignment explanation
Indices: 26936--28102 Score: 1523
Period size: 390 Copynumber: 3.0 Consensus size: 387
26926 ATGCTTTAAA
* * * * *
26936 AAATATTTGATGCGCTGCCTCCACTGAAAGAGGTTGTGCATGATGTTCCCAATTTTAATCATGAG
1 AAATATCTGAGGCGCTGCCTCCACTGAAAGAGGTCGTGCATGATGTTCTCAATTTTGATCATGAG
* * * * *
27001 GACCTATGTACTATGGTCAACCATGATGAGTTTAATGGTGAAATTAAACAAGAGTCAGAAATTAG
66 GACCTTTGTACTATCGTCAACCATGATGAGTTTAATGGTGAAATTAAACAAGAGTCTGGAA-CAG
27066 AGATCAT-GAGGATGATTTGAATATAGTTGAAGCGGTCTCCAATCATATTGACATAGCAGCAAAT
130 AGATCATGGA-GATGATTTGAATATAGTTGAAGCGGTCTCCAATCA-ATTGACATAGCAGCAAAT
* ** * *
27130 GTAACCGTCA-ATGTAGAAGTATTAGATCATCTAACCATTACCATGGAGCTTAAACTGATTCTGA
193 GTAACTGT-AGATGTAGAAGTAACAGATAATCTAACCACTACCATGGAGCTTAAACTGATTCTGA
* * * *
27194 ATGAAAGTGTAGAAAAGCCAATACAATTTCTGGCCAAGATTGAAGATATGCCAA-CTAAAGAGGT
257 ATGAAAGTGTAGAAGAGCCAATACACTTTCTGGCCAAGATTGAAGAGATGCCAACCGAAA-AGGT
** * ** *
27258 TAAAGAGTTTGTTTAAAATTCTCATTCGATGATAGAGGGAAAGCTCAAGCAATTGAAACTTCACG
321 CGAAGAGTTCGTTT--AATTCTCATTCGATGATAGA-GGAAAGCTCAAGCAATCAAAAGTTCACG
27323 CCAAC
383 CCAAC
* * * *
27328 AAATATCTAAGGCGTTACCTCCACTGAAAGAGGTCGTGCATGATGTT-TCCAATTCTGATCATGA
1 AAATATCTGAGGCGCTGCCTCCACTGAAAGAGGTCGTGCATGATGTTCT-CAATTTTGATCATGA
* * *
27392 GGATCTTTGTACTATCATCAACCATGATGAGTTTAATGGTGAAATTAAATAAGAGTCTGGAACTA
65 GGACCTTTGTACTATCGTCAACCATGATGAGTTTAATGGTGAAATTAAACAAGAGTCTGGAAC-A
* * ** **
27457 GAGATCAAGGGGATGATTTGAATATAGTTGAAATGGTCTCCAATCCAATTGACATAATAGCAAAT
129 GAGATCATGGAGATGATTTGAATATAGTTGAAGCGGTCTCCAAT-CAATTGACATAGCAGCAAAT
* * * * * *
27522 GCAACTGTAGATGTAGAAGTAACAGATGATCTAACCACTACCTTAGAGCTTAAACTGGTTTTGAA
193 GTAACTGTAGATGTAGAAGTAACAGATAATCTAACCACTACCATGGAGCTTAAACTGATTCTGAA
* * *
27587 TGAAAGTGTAGAAGAGCTAATACACTTTCTGGCCAAGATTGAAGAGGTTCCAACCGAAAAGGTCG
258 TGAAAGTGTAGAAGAGCCAATACACTTTCTGGCCAAGATTGAAGAGATGCCAACCGAAAAGGTCG
* * ** *
27652 AAGAGTTCGTTTCATTCTCATTCGATGATAGAGTGAAAGCTCGAGCAATCAAAAGTTCATTCCTA
323 AAGAGTTCGTTTAATTCTCATTCGATGATAGAG-GAAAGCTCAAGCAATCAAAAGTTCACGCCAA
*
27717 T
387 C
* * * *
27718 AAATATCTGAGGCACTGCCTCAATTGAAAGAGGTCGTGCATGATGTTCTCAATTTTGATCATAAG
1 AAATATCTGAGGCGCTGCCTCCACTGAAAGAGGTCGTGCATGATGTTCTCAATTTTGATCATGAG
* * * *
27783 GACCTTTGCACTATCGTCAACCATGATGAGTTTAATGGTGAAATTCAACAAGAGTTTGGAACCGT
66 GACCTTTGTACTATCGTCAACCATGATGAGTTTAATGGTGAAATTAAACAAGAGTCTGGAACAG-
* ** *
27848 AGATCATGGAGATGATTTGAATATAATTGAAGCAATCTCCAATATAATTGACATAGCAGCAAATG
130 AGATCATGGAGATGATTTGAATATAGTTGAAGCGGTCTCCAAT-CAATTGACATAGCAGCAAATG
*
27913 TTACTGTAGATGTAGAAGTAACAGATAATCTAACCACTACCATGGAGCTTAAACTGATTCTGAAT
194 TAACTGTAGATGTAGAAGTAACAGATAATCTAACCACTACCATGGAGCTTAAACTGATTCTGAAT
* * *
27978 GAAAGTGTAGAAGATCCAATACACTTTCTGGCCAAGATTGAAGAGATGCCAACTGAAGAGGTCGA
259 GAAAGTGTAGAAGAGCCAATACACTTTCTGGCCAAGATTGAAGAGATGCCAACCGAAAAGGTCGA
* * * *
28043 AGAGTTCATTTAATTCTCATTCGATGATAGAGGGAAGCCCAAGAAATCAAAAGTTCACGC
324 AGAGTTCGTTTAATTCTCATTCGATGATAGAGGAAAGCTCAAGCAATCAAAAGTTCACGC
28103 GACGTGGAGT
Statistics
Matches: 667, Mismatches: 99, Indels: 21
0.85 0.13 0.03
Matches are distributed among these distances:
389 24 0.04
390 355 0.53
391 2 0.00
392 279 0.42
393 7 0.01
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (387 bp):
AAATATCTGAGGCGCTGCCTCCACTGAAAGAGGTCGTGCATGATGTTCTCAATTTTGATCATGAG
GACCTTTGTACTATCGTCAACCATGATGAGTTTAATGGTGAAATTAAACAAGAGTCTGGAACAGA
GATCATGGAGATGATTTGAATATAGTTGAAGCGGTCTCCAATCAATTGACATAGCAGCAAATGTA
ACTGTAGATGTAGAAGTAACAGATAATCTAACCACTACCATGGAGCTTAAACTGATTCTGAATGA
AAGTGTAGAAGAGCCAATACACTTTCTGGCCAAGATTGAAGAGATGCCAACCGAAAAGGTCGAAG
AGTTCGTTTAATTCTCATTCGATGATAGAGGAAAGCTCAAGCAATCAAAAGTTCACGCCAAC
Found at i:32830 original size:6 final size:6
Alignment explanation
Indices: 32819--32855 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
32809 AGTTTAAGAT
* *
32819 ACCATC ACCATC ACCATC ACCATC AACATC AACATC A
1 ACCATC ACCATC ACCATC ACCATC ACCATC ACCATC A
32856 AAATCTCCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.41, C:0.43, G:0.00, T:0.16
Consensus pattern (6 bp):
ACCATC
Found at i:34613 original size:105 final size:105
Alignment explanation
Indices: 34431--34643 Score: 349
Period size: 105 Copynumber: 2.0 Consensus size: 105
34421 CTACAACCTT
34431 TTCCCATAATCTTTTCAGCCTTCATAGCAGAAACCACATTAGACATAAAACCCGATCTTTCACCA
1 TTCCCATAATCTTTTCAGCCTTCATAGCAGAAACCACATTAGACATAAAACCCGATCTTTCACCA
*
34496 CCAACAATAATTTCCAACCTATCATTATTCCTTAGAGTTA
66 CCAACAATAATTTCCAACCCATCATTATTCCTTAGAGTTA
* *
34536 TTCCCATAATCTTTTCAGCCTTCATTGTC-GAAACCACATTATACATAAAACCC-AGTCTTTCAC
1 TTCCCATAATCTTTTCAGCCTTCATAG-CAGAAACCACATTAGACATAAAACCCGA-TCTTTCAC
* *
34599 TACCAACAATAATTTCCAACCCATCATTATTCTTTAGAGTTA
64 CACCAACAATAATTTCCAACCCATCATTATTCCTTAGAGTTA
34641 TTC
1 TTC
34644 ACTTAGTTTT
Statistics
Matches: 101, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
104 1 0.01
105 99 0.98
106 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.06, T:0.33
Consensus pattern (105 bp):
TTCCCATAATCTTTTCAGCCTTCATAGCAGAAACCACATTAGACATAAAACCCGATCTTTCACCA
CCAACAATAATTTCCAACCCATCATTATTCCTTAGAGTTA
Found at i:38951 original size:15 final size:15
Alignment explanation
Indices: 38931--38975 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
38921 TATGATATTG
38931 TATCTTGGATTTCTT
1 TATCTTGGATTTCTT
* *
38946 TATCTTGGATTTATC
1 TATCTTGGATTTCTT
*
38961 TATCTTGGACTTCTT
1 TATCTTGGATTTCTT
38976 AATCCTATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.13, T:0.56
Consensus pattern (15 bp):
TATCTTGGATTTCTT
Found at i:41153 original size:37 final size:37
Alignment explanation
Indices: 41094--41459 Score: 597
Period size: 37 Copynumber: 9.9 Consensus size: 37
41084 AGCTCAGACG
* * *
41094 AAATCTCCACATGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
41131 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* * *
41168 TAATCTTCACACGTAGTCATCGGGTCTTACCCGGAAA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
41205 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* * *
41242 TAATCTTCACACGTAGTCATCGGGTCTTACCCGGAAA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
41279 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* * *
41316 TAATCTTCACACGTAGTCATCGGGTCTTACCCGGAAA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
41353 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* * *
41390 TAATCTTCACACGTAGTCATCGGGTCTTACCCGGAAA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
41427 AAATCTCCACACGTAGTCATCGGGTCTTACCCG
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCG
41460 AAATATATTT
Statistics
Matches: 303, Mismatches: 26, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 303 1.00
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:41195 original size:74 final size:74
Alignment explanation
Indices: 41112--41459 Score: 687
Period size: 74 Copynumber: 4.7 Consensus size: 74
41102 ACATGAAGTT
*
41112 ATCGGGTCTTACCCGGACAAAATCTCCACACGTAGTCATCGGGTCTTACCCGGACATAATCTTCA
1 ATCGGGTCTTACCCGGAAAAAATCTCCACACGTAGTCATCGGGTCTTACCCGGACATAATCTTCA
41177 CACGTAGTC
66 CACGTAGTC
41186 ATCGGGTCTTACCCGGAAAAAATCTCCACACGTAGTCATCGGGTCTTACCCGGACATAATCTTCA
1 ATCGGGTCTTACCCGGAAAAAATCTCCACACGTAGTCATCGGGTCTTACCCGGACATAATCTTCA
41251 CACGTAGTC
66 CACGTAGTC
41260 ATCGGGTCTTACCCGGAAAAAATCTCCACACGTAGTCATCGGGTCTTACCCGGACATAATCTTCA
1 ATCGGGTCTTACCCGGAAAAAATCTCCACACGTAGTCATCGGGTCTTACCCGGACATAATCTTCA
41325 CACGTAGTC
66 CACGTAGTC
41334 ATCGGGTCTTACCCGGAAAAAATCTCCACACGTAGTCATCGGGTCTTACCCGGACATAATCTTCA
1 ATCGGGTCTTACCCGGAAAAAATCTCCACACGTAGTCATCGGGTCTTACCCGGACATAATCTTCA
41399 CACGTAGTC
66 CACGTAGTC
41408 ATCGGGTCTTACCCGGAAAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
1 ATCGGGTCTTACCCGGAAAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
41460 AAATATATTT
Statistics
Matches: 273, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 273 1.00
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.24
Consensus pattern (74 bp):
ATCGGGTCTTACCCGGAAAAAATCTCCACACGTAGTCATCGGGTCTTACCCGGACATAATCTTCA
CACGTAGTC
Found at i:41658 original size:46 final size:46
Alignment explanation
Indices: 41605--41695 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
41595 TATATATACA
* * *
41605 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATCTCACATTAGCCATTCGGCCTTACCACATATC
* * *
41651 CATCTCATACACGTTTCGCATTAGCCATTCGGCCTTACCACATAT
1 CATCTCATACACATCTCACATTAGCCATTCGGCCTTACCACATAT
41696 ATTCATGTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.26, C:0.32, G:0.09, T:0.33
Consensus pattern (46 bp):
CATCTCATACACATCTCACATTAGCCATTCGGCCTTACCACATATC
Found at i:41846 original size:205 final size:205
Alignment explanation
Indices: 41494--41917 Score: 834
Period size: 205 Copynumber: 2.1 Consensus size: 205
41484 CAATTAATCA
41494 CATGTTACAACATTCACATCGACTGTCACATTTTTAATTCATTTGCCTCATAAAAAATCTAATAA
1 CATGTTACAACATTCACATCGACTGTCACATTTTTAATTCATTTGCCTCATAAAAAATCTAATAA
41559 TACACAACTTTCACCGTTTGTCATTTGGCCACAATATATATATACACATCTCATACATATCTCAC
66 TACACAACTTTCACCGTTTGTCATTTGGCCACAATATATATATACACATCTCATACATATCTCAC
41624 ATTAGCCATTTGGCTTTACCACATATCCATCTCATACACGTTTCGCATTAGCCATTCGGCCTTAC
131 ATTAGCCATTTGGCTTTACCACATATCCATCTCATACACGTTTCGCATTAGCCATTCGGCCTTAC
41689 CACATATATT
196 CACATATATT
41699 CATGTTACAACATTCACATCGACTGTCACATTTTTAATTCATTTGCCTCATAAAAAATCTAATAA
1 CATGTTACAACATTCACATCGACTGTCACATTTTTAATTCATTTGCCTCATAAAAAATCTAATAA
41764 TACACAACTTTCACCGTTTGTCATTTGGCCACAATATATATATACACATCTCATACATATCTCAC
66 TACACAACTTTCACCGTTTGTCATTTGGCCACAATATATATATACACATCTCATACATATCTCAC
41829 ATTAGCCATTTGGCTTTACCACATATCCATCTCATACACGTTTCGCATTAGCCATTCGGCCTTAC
131 ATTAGCCATTTGGCTTTACCACATATCCATCTCATACACGTTTCGCATTAGCCATTCGGCCTTAC
41894 CACATATATT
196 CACATATATT
41904 CATGTT-C-ACATTCA
1 CATGTTACAACATTCA
41918 TCACATTGGC
Statistics
Matches: 219, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
203 7 0.03
204 1 0.00
205 211 0.96
ACGTcount: A:0.31, C:0.26, G:0.08, T:0.35
Consensus pattern (205 bp):
CATGTTACAACATTCACATCGACTGTCACATTTTTAATTCATTTGCCTCATAAAAAATCTAATAA
TACACAACTTTCACCGTTTGTCATTTGGCCACAATATATATATACACATCTCATACATATCTCAC
ATTAGCCATTTGGCTTTACCACATATCCATCTCATACACGTTTCGCATTAGCCATTCGGCCTTAC
CACATATATT
Found at i:41863 original size:46 final size:46
Alignment explanation
Indices: 41810--41944 Score: 132
Period size: 46 Copynumber: 2.9 Consensus size: 46
41800 TATATATACA
* * *
41810 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATCTCACATTAGCCATTCGGCCTTACCACATATC
* * *
41856 CATCTCATACACGTTTCGCATTAGCCATTCGGCCTTACCACATAT-
1 CATCTCATACACATCTCACATTAGCCATTCGGCCTTACCACATATC
* * *
41901 -AT-TCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACA
1 CATCTCA--TACACA-TC-TCACATTAGCCATTCGGCCTTACCACA
41945 CATACGCATG
Statistics
Matches: 73, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
43 3 0.04
44 2 0.03
45 4 0.05
46 40 0.55
47 24 0.33
ACGTcount: A:0.26, C:0.31, G:0.10, T:0.33
Consensus pattern (46 bp):
CATCTCATACACATCTCACATTAGCCATTCGGCCTTACCACATATC
Found at i:41936 original size:47 final size:47
Alignment explanation
Indices: 41874--41970 Score: 140
Period size: 47 Copynumber: 2.1 Consensus size: 47
41864 ACACGTTTCG
* ** *
41874 CATTAGCCATTCGGCCTTACCACATATATTCATGTTCACATTCATCA
1 CATTAGCCATTCGGCCTTACCACACATACGCATGTTCACATCCATCA
* *
41921 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTAGCCATTCGGCCTTACCACACATACGCATGTTCACATCCATCA
41968 CAT
1 CAT
41971 AAAATCCTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.27, C:0.32, G:0.10, T:0.31
Consensus pattern (47 bp):
CATTAGCCATTCGGCCTTACCACACATACGCATGTTCACATCCATCA
Found at i:44763 original size:28 final size:27
Alignment explanation
Indices: 44700--44851 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
44690 ATATTAAGTC
* * *
44700 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
44727 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
44755 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
44782 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
44810 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
44837 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
44852 GCACAATTTA
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:44784 original size:55 final size:55
Alignment explanation
Indices: 44700--44851 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
44690 ATATTAAGTC
* * *
44700 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
44755 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
44810 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
44852 GCACAATTTA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:57495 original size:50 final size:50
Alignment explanation
Indices: 57376--57758 Score: 417
Period size: 50 Copynumber: 7.6 Consensus size: 50
57366 GTTGTGATAA
* * *** *
57376 CACATGTGTAGTACTATGTGCAGGCTACTATGTGTTTAAGATAGTTTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAT--TGTTAGGT
*
57428 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
* ** * * * * * *
57478 CGCATGTGTAGTACTAAGTATAGGCTGCTATGCGTACTC-GATAGTTTCGAT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTAC-CAGATTG-TTAGGT
* * *
57529 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
* * * * * *
57579 CACGTGTGTGGTCCTAAGTGCATGCTACTACGTGTACCAGATTGATAGGA
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
* * * * * *
57629 CGCATGTGTAGTACTAATTGCAGGCTACTACGTGTATCAGATGGATAAGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
* *
57679 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGATACGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
*
57729 CGCATGTGTAGTACTAAGTGCAGGCTACTA
1 CACATGTGTAGTACTAAGTGCAGGCTACTA
57759 TGCATACCCG
Statistics
Matches: 277, Mismatches: 51, Indels: 8
0.82 0.15 0.02
Matches are distributed among these distances:
50 203 0.73
51 38 0.14
52 36 0.13
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (50 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
Found at i:57990 original size:16 final size:16
Alignment explanation
Indices: 57969--58000 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
57959 TGAATGGAAT
57969 AAGTGAAATTATGTAA
1 AAGTGAAATTATGTAA
*
57985 AAGTGAAATTTTGTAA
1 AAGTGAAATTATGTAA
58001 TAAAACAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (16 bp):
AAGTGAAATTATGTAA
Found at i:59764 original size:18 final size:19
Alignment explanation
Indices: 59736--59779 Score: 81
Period size: 18 Copynumber: 2.4 Consensus size: 19
59726 CCCGTATGGA
59736 CAAATCATATACATAAAAC
1 CAAATCATATACATAAAAC
59755 CAAA-CATATACATAAAAC
1 CAAATCATATACATAAAAC
59773 CAAATCA
1 CAAATCA
59780 GCCACAACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.59, C:0.23, G:0.00, T:0.18
Consensus pattern (19 bp):
CAAATCATATACATAAAAC
Found at i:60417 original size:43 final size:42
Alignment explanation
Indices: 60370--60450 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
60360 TCTATGTAAT
*
60370 CTCATATCGATGCCAATAGCCCAGTTATGGTCTTACATGAAGC
1 CTCATATCGATGCC-ATAGCCCAGATATGGTCTTACATGAAGC
*
60413 CTCATATCGATGCCATATCCCAGATATGGTCTTACATG
1 CTCATATCGATGCCATAGCCCAGATATGGTCTTACATG
60451 TAATCTTAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
42 22 0.61
43 14 0.39
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (42 bp):
CTCATATCGATGCCATAGCCCAGATATGGTCTTACATGAAGC
Found at i:60446 original size:42 final size:42
Alignment explanation
Indices: 60339--60453 Score: 144
Period size: 43 Copynumber: 2.7 Consensus size: 42
60329 CCATACCAAA
* * *
60339 GCCATATCCCAGGTATGGACTT-CTATGTAATCTCATATCGAT
1 GCCATATCCCAGATATGGTCTTAC-ATGTAACCTCATATCGAT
* *
60381 GCCAATAGCCCAGTTATGGTCTTACATG-AAGCCTCATATCGAT
1 GCC-ATATCCCAGATATGGTCTTACATGTAA-CCTCATATCGAT
60424 GCCATATCCCAGATATGGTCTTACATGTAA
1 GCCATATCCCAGATATGGTCTTACATGTAA
60454 TCTTAGTAAC
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
42 27 0.43
43 35 0.56
44 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (42 bp):
GCCATATCCCAGATATGGTCTTACATGTAACCTCATATCGAT
Found at i:67318 original size:43 final size:40
Alignment explanation
Indices: 67256--67375 Score: 141
Period size: 43 Copynumber: 2.8 Consensus size: 40
67246 TACCATGCCA
67256 ATGCCATATCCCAAATATGGTCTTACATGTAATCTCATATCG
1 ATGCCATATCCC-AATATGGTCTTACA-GTAATCTCATATCG
* **
67298 ATGCCAATAACCCAACTATGGTCTTACACAAAGTCTCATATCG
1 ATGCC-ATATCCCAA-TATGGTCTTACAGTAA-TCTCATATCG
*
67341 ATGCCATATCTCAGATATGGTCTTACACGTAATCT
1 ATGCCATATCCCA-ATATGGTCTTACA-GTAATCT
67376 TAGTTACCCT
Statistics
Matches: 66, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
42 30 0.45
43 36 0.55
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.31
Consensus pattern (40 bp):
ATGCCATATCCCAATATGGTCTTACAGTAATCTCATATCG
Found at i:69082 original size:20 final size:21
Alignment explanation
Indices: 69057--69096 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
69047 TCAAGCTGAC
*
69057 AAGGGC-ACACGCCCGTGTGG
1 AAGGGCAACACGCCCATGTGG
69077 AAGGGCAACACGCCCATGTG
1 AAGGGCAACACGCCCATGTG
69097 TCTTCTTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.25, C:0.30, G:0.35, T:0.10
Consensus pattern (21 bp):
AAGGGCAACACGCCCATGTGG
Found at i:72588 original size:51 final size:51
Alignment explanation
Indices: 72508--72612 Score: 147
Period size: 51 Copynumber: 2.1 Consensus size: 51
72498 TAGTAAATGT
* * **
72508 CTTCCAATCAGGCTCAAGATGAGTCCGAGGGAGCTGAGAACCATGCTCCAG
1 CTTCCAATCAAGCTCAAGATAAGTCCGAGGGAGCCAAGAACCATGCTCCAG
* * *
72559 CTTCCGATCAAGCTCAAGATAAGTTCGAGGGAGCCAAGAGCCATGCTCCAG
1 CTTCCAATCAAGCTCAAGATAAGTCCGAGGGAGCCAAGAACCATGCTCCAG
72610 CTT
1 CTT
72613 TCGTTTAGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (51 bp):
CTTCCAATCAAGCTCAAGATAAGTCCGAGGGAGCCAAGAACCATGCTCCAG
Found at i:81299 original size:48 final size:48
Alignment explanation
Indices: 81248--81569 Score: 259
Period size: 48 Copynumber: 6.7 Consensus size: 48
81238 TGAGTAGCCA
* * * * *
81248 ATGCCATGTTCCAAACATGGCCTTACACTGGCTCACATGTCGAGGCCA
1 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATCTCAAGGCCG
** * **
81296 ATGCCATGTCCCAAACATGGTCTTACACTATCTCTA-GTCTCAATACCG
1 ATGCCATGTCCCAAACATGGTCTTACACTGGCTC-ACATCTCAAGGCCG
* * * * * *
81344 ATGCCATGTCCTAGACATGGTCGTACAGTGGCTCACATGTCGAGGCCG
1 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATCTCAAGGCCG
* * * *
81392 ATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCGTCTCAATGCCG
1 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATCTCAAGGCCG
* * ** ** * *
81440 ATGCCATATCCCAAACATGGTCTTACATTGGCTTTCATAACATGGTCG
1 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATCTCAAGGCCG
* ** * * * * *
81488 ATGCCATGTCTCGGACATGGTCTTACACTAGCGCACATATCAATGCCA
1 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATCTCAAGGCCG
* * ** *
81536 ATGCCATTTCCCAGACATAATCTTACACTAGCTC
1 ATGCCATGTCCCAAACATGGTCTTACACTGGCTC
81570 TCACAACATT
Statistics
Matches: 211, Mismatches: 61, Indels: 4
0.76 0.22 0.01
Matches are distributed among these distances:
47 1 0.00
48 209 0.99
49 1 0.00
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (48 bp):
ATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATCTCAAGGCCG
Found at i:81412 original size:96 final size:95
Alignment explanation
Indices: 81248--81519 Score: 339
Period size: 96 Copynumber: 2.8 Consensus size: 95
81238 TGAGTAGCCA
* *
81248 ATGCCATGTTCCAAACATGGCCTTACACTGGCTCACATGTCGAGGCCAATGCCATGTCCCAAACA
1 ATGCCATG-TCCAAACATGGTCTTACACTGGCTCACATGTCGAGGCCGATGCCATGTCCCAAACA
*
81313 TGGTCTTACACTATCTCTAGTCTCAATACCG
65 TGGTCTTACACTAGCTCTAGTCTCAATACCG
* * *
81344 ATGCCATGTCCTAGACATGGTCGTACAGTGGCTCACATGTCGAGGCCGATGCCATGTCCCAAACA
1 ATGCCATGTCC-AAACATGGTCTTACACTGGCTCACATGTCGAGGCCGATGCCATGTCCCAAACA
* *
81409 TGGTCTTACACTAGCTCTCGTCTCAATGCCG
65 TGGTCTTACACTAGCTCTAGTCTCAATACCG
* * ** ** * * **
81440 ATGCCATATCCCAAACATGGTCTTACATTGGCTTTCATAAC-ATGGTCGATGCCATGTCTCGGAC
1 ATGCCATGT-CCAAACATGGTCTTACACTGGCTCACATGTCGA-GGCCGATGCCATGTCCCAAAC
81504 ATGGTCTTACACTAGC
64 ATGGTCTTACACTAGC
81520 GCACATATCA
Statistics
Matches: 153, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
95 4 0.03
96 147 0.96
97 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.27
Consensus pattern (95 bp):
ATGCCATGTCCAAACATGGTCTTACACTGGCTCACATGTCGAGGCCGATGCCATGTCCCAAACAT
GGTCTTACACTAGCTCTAGTCTCAATACCG
Found at i:81531 original size:96 final size:96
Alignment explanation
Indices: 81387--81625 Score: 280
Period size: 96 Copynumber: 2.5 Consensus size: 96
81377 CACATGTCGA
* * * * * *
81387 GGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCGTCTCAATGCCGATGCCATATCCC
1 GGCCGATGCCATGTCTCAAACATGGTCTTACACTAGCACACATATCAATGCCAATGCCATATCCC
** * * * *
81452 AAACATGGTCTTACATTGGCTTTCATAACAT
66 AAACATAATCTTACACTAGCTCTCACAACAT
* ** * *
81483 GGTCGATGCCATGTCTCGGACATGGTCTTACACTAGCGCACATATCAATGCCAATGCCATTTCCC
1 GGCCGATGCCATGTCTCAAACATGGTCTTACACTAGCACACATATCAATGCCAATGCCATATCCC
*
81548 AGACATAATCTTACACTAGCTCTCACAACAT
66 AAACATAATCTTACACTAGCTCTCACAACAT
* * * *
81579 TGCCGATGTCATGTTTCAAACATGGTCCTACACTAGCACACATATCA
1 GGCCGATGCCATGTCTCAAACATGGTCTTACACTAGCACACATATCA
81626 CCCAAATGTC
Statistics
Matches: 118, Mismatches: 25, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
96 118 1.00
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (96 bp):
GGCCGATGCCATGTCTCAAACATGGTCTTACACTAGCACACATATCAATGCCAATGCCATATCCC
AAACATAATCTTACACTAGCTCTCACAACAT
Found at i:81583 original size:144 final size:144
Alignment explanation
Indices: 81342--81610 Score: 317
Period size: 144 Copynumber: 1.9 Consensus size: 144
81332 GTCTCAATAC
* * * * * *
81342 CGATGCCATGTCCTAGACATGGTCGTACAGTGGCTCACATGTCGAGGCCGATGCCATGTCCCAAA
1 CGATGCCATGTCCTAGACATGGTCGTACACTAGCGCACATATCAAGGCCAATGCCATGTCCCAAA
** * * *
81407 CATGGTCTTACACTAGCTCTCGTCTCAATGCCGATGCCATATCCCAAACATGGTCTTACATTGGC
66 CATAATCTTACACTAGCTCTCGACACAATGCCGATGCCATATCCCAAACATGGTCCTACATTGGC
81472 TTTCATAACATGGT
131 TTTCATAACATGGT
* * * * *
81486 CGATGCCATGT-CTCGGACATGGTCTTACACTAGCGCACATATCAATGCCAATGCCATTTCCCAG
1 CGATGCCATGTCCT-AGACATGGTCGTACACTAGCGCACATATCAAGGCCAATGCCATGTCCCAA
* * * **
81550 ACATAATCTTACACTAGCTCTC-ACAACATTGCCGATGTCATGTTTCAAACATGGTCCTACA
65 ACATAATCTTACACTAGCTCTCGAC-ACAATGCCGATGCCATATCCCAAACATGGTCCTACA
81611 CTAGCACACA
Statistics
Matches: 102, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
143 3 0.03
144 99 0.97
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (144 bp):
CGATGCCATGTCCTAGACATGGTCGTACACTAGCGCACATATCAAGGCCAATGCCATGTCCCAAA
CATAATCTTACACTAGCTCTCGACACAATGCCGATGCCATATCCCAAACATGGTCCTACATTGGC
TTTCATAACATGGT
Found at i:89146 original size:48 final size:48
Alignment explanation
Indices: 89077--89259 Score: 190
Period size: 48 Copynumber: 3.8 Consensus size: 48
89067 AAGTCGAAAT
**
89077 CGATGCCATGCCCCAGACATGGTCTTACACTAGCTCTCATCTCAATAC
1 CGATGCCATGTACCAGACATGGTCTTACACTAGCTCTCATCTCAATAC
* * * * * * * **
89125 TGATGCTATGTACTAGACATGGTCTTACACTGGCTCACATGTCGAGGC
1 CGATGCCATGTACCAGACATGGTCTTACACTAGCTCTCATCTCAATAC
* * **
89173 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCGTCTCAATGT
1 CGATGCCATGTACCAGACATGGTCTTACACTAGCTCTCATCTCAATAC
* *
89221 CGATGCCATGT-CCCGAACATGGTCTTACACTGGCT-TCAT
1 CGATGCCATGTACCAG-ACATGGTCTTACACTAGCTCTCAT
89260 AATGTGGCCA
Statistics
Matches: 109, Mismatches: 25, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
47 6 0.06
48 103 0.94
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (48 bp):
CGATGCCATGTACCAGACATGGTCTTACACTAGCTCTCATCTCAATAC
Found at i:89194 original size:96 final size:96
Alignment explanation
Indices: 89029--89289 Score: 311
Period size: 96 Copynumber: 2.7 Consensus size: 96
89019 AGGTGAATTG
* * *** *
89029 TCGATGCCATGTTCCA-AACATGGTTTTACACTGGC-CAAAAGTCGAAATCGATGCCATGCCCCA
1 TCGATGCCATG-TCCAGAACATGGTCTTACACTGGCTCAAATGTCGAGGCCGATGCCATGTCCCA
89092 GACATGGTCTTACACTAGCTCTCATCTCAATAC
65 GACATGGTCTTACACTAGCTCTCATCTCAAT-C
* * *
89125 T-GATGCTATGTACTAG-ACATGGTCTTACACTGGCTCACATGTCGAGGCCGATGCCATGTCCCA
1 TCGATGCCATGT-CCAGAACATGGTCTTACACTGGCTCAAATGTCGAGGCCGATGCCATGTCCCA
* *
89188 GACATGGTCTTACACTAGCTCTCGTCTCAATG
65 GACATGGTCTTACACTAGCTCTCATCTCAATC
* *
89220 TCGATGCCATGTCCCGAACATGGTCTTACACTGGCTTCATAATGT---GGCCAATGCCATGTCCC
1 TCGATGCCATGTCCAGAACATGGTCTTACACTGGC-TCA-AATGTCGAGGCCGATGCCATGTCCC
89282 AGACATGG
64 AGACATGG
89290 ACATATCAAT
Statistics
Matches: 142, Mismatches: 16, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
94 1 0.01
95 54 0.38
96 80 0.56
97 3 0.02
98 4 0.03
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (96 bp):
TCGATGCCATGTCCAGAACATGGTCTTACACTGGCTCAAATGTCGAGGCCGATGCCATGTCCCAG
ACATGGTCTTACACTAGCTCTCATCTCAATC
Found at i:89308 original size:34 final size:34
Alignment explanation
Indices: 89270--89355 Score: 163
Period size: 34 Copynumber: 2.5 Consensus size: 34
89260 AATGTGGCCA
89270 ATGCCATGTCCCAGACATGGACATATCAATGTCG
1 ATGCCATGTCCCAGACATGGACATATCAATGTCG
89304 ATGCCATGTCCCAGACATGGACATATCAATGTCG
1 ATGCCATGTCCCAGACATGGACATATCAATGTCG
*
89338 ATGCCATGTCCCAAACAT
1 ATGCCATGTCCCAGACAT
89356 TGTCTTACAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (34 bp):
ATGCCATGTCCCAGACATGGACATATCAATGTCG
Found at i:109167 original size:21 final size:21
Alignment explanation
Indices: 109143--109191 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
109133 TCAAATGGAG
*
109143 TAAAGAAATCTTGTA-ATGAAA
1 TAAA-AAATCTTGAACATGAAA
*
109164 TAAAAAAACTTGAACATGAAA
1 TAAAAAATCTTGAACATGAAA
109185 -AAAAAAT
1 TAAAAAAT
109192 GAAAATTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.61, C:0.06, G:0.10, T:0.22
Consensus pattern (21 bp):
TAAAAAATCTTGAACATGAAA
Found at i:116960 original size:20 final size:19
Alignment explanation
Indices: 116913--116965 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
116903 AATGAATGTG
* *
116913 ATGGATGGCATATATGTTTA
1 ATGGATGACA-ATATGATTA
116933 ATGGATGA-AATATGATTA
1 ATGGATGACAATATGATTA
116951 ATGTGTATGACAATA
1 ATG-G-ATGACAATA
116966 AATGTAGTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 11 0.39
19 2 0.07
20 11 0.39
21 4 0.14
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.36
Consensus pattern (19 bp):
ATGGATGACAATATGATTA
Found at i:117964 original size:64 final size:64
Alignment explanation
Indices: 117856--117975 Score: 159
Period size: 64 Copynumber: 1.9 Consensus size: 64
117846 CGATCACTAT
* * ** * *
117856 TGATCCTGGATGTGTTGCAGACATACCGTAGGTCTTTTTAAGCATTCTATTATATGATTGGTAG
1 TGATCATGCATGTGTTGCAGACATACCGTAACTCTTTATAAGCATCCTATTATATGATTGGTAG
* * *
117920 TGATCATGCATGTGTTGCGGGCATACCGTAACTCTTTATGAGCATCCTATTATATG
1 TGATCATGCATGTGTTGCAGACATACCGTAACTCTTTATAAGCATCCTATTATATG
117976 GCTCTCCAGA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
64 47 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.38
Consensus pattern (64 bp):
TGATCATGCATGTGTTGCAGACATACCGTAACTCTTTATAAGCATCCTATTATATGATTGGTAG
Found at i:125504 original size:180 final size:180
Alignment explanation
Indices: 125200--125559 Score: 612
Period size: 180 Copynumber: 2.0 Consensus size: 180
125190 AATATGAGAT
*
125200 GATGATATATGAACATGGAATTTACTTGATGAATATGGTCATCCATGATCATAGATTTGTACACC
1 GATGATATATGAACATGGAATTTACTTGATGAATATGGTCATCCATGATCATAGATTTGAACACC
* * *
125265 TTGAATGTACTACCTGTGTGACACTGACATTTCAAATGATTTAATGGGAAAAGTTCTGACATGAA
66 TTGAACGTACTACCTGTGTGACACTAACATTTCAAATGATTTAATGGGAAAACTTCTGACATGAA
* **
125330 ATAGTTTGAACTCGAGATGAATTATTATGAAAATGTACTTTAAATACAAG
131 ATAGTCTGAACTCGAGACAAATTATTATGAAAATGTACTTTAAATACAAG
*
125380 GATGATATATGAACATGGAATTTACTTGATGAATATGGTCATCCGTGATCATAGATTTGAACACC
1 GATGATATATGAACATGGAATTTACTTGATGAATATGGTCATCCATGATCATAGATTTGAACACC
* * *
125445 TTTAGCGTACTACCTGTGTGACACTAACATTTCAAATGATTTAATGGGCAAACTTCTGACATGAA
66 TTGAACGTACTACCTGTGTGACACTAACATTTCAAATGATTTAATGGGAAAACTTCTGACATGAA
*
125510 ATAGTCTGAACTCGGGACAAATTATTATGAAAATGTACTTTAAATACAAG
131 ATAGTCTGAACTCGAGACAAATTATTATGAAAATGTACTTTAAATACAAG
125560 AATATGATTT
Statistics
Matches: 168, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
180 168 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.33
Consensus pattern (180 bp):
GATGATATATGAACATGGAATTTACTTGATGAATATGGTCATCCATGATCATAGATTTGAACACC
TTGAACGTACTACCTGTGTGACACTAACATTTCAAATGATTTAATGGGAAAACTTCTGACATGAA
ATAGTCTGAACTCGAGACAAATTATTATGAAAATGTACTTTAAATACAAG
Found at i:127972 original size:27 final size:27
Alignment explanation
Indices: 127940--128366 Score: 281
Period size: 27 Copynumber: 16.0 Consensus size: 27
127930 AAACATACAT
* **
127940 CACATAGGGGCAAAATAGTCATCCTAC
1 CACATAAGGGCAAAATAGTCATTTTAC
127967 CACATAAGGG-AAAATTAGTCATTTTAC
1 CACATAAGGGCAAAA-TAGTCATTTTAC
* * * *
127994 CTCATAAGGGAAAAATTGTCATTTTAT
1 CACATAAGGGCAAAATAGTCATTTTAC
* *
128021 CACATAAGGGC-AAATCCGTCATTTTAA
1 CACATAAGGGCAAAAT-AGTCATTTTAC
* * * *
128048 CAC-CAA-GGCAAAACAATCATTTTGC
1 CACATAAGGGCAAAATAGTCATTTTAC
* * *
128073 CACATAAGGGAAAAATTGTCATTTTAT
1 CACATAAGGGCAAAATAGTCATTTTAC
* * *
128100 CACATAAGGGCAAAATCA-TTATGTTAA
1 CACATAAGGGCAAAAT-AGTCATTTTAC
*
128127 CACATAA-GGCAAAAACAGTCATTTTGA-
1 CACATAAGGGC-AAAATAGTCATTTT-AC
* * * *
128154 CACATAAGGGTAAAACATTCATTTTGC
1 CACATAAGGGCAAAATAGTCATTTTAC
* * ** *
128181 CATATAAGGGAAAAACCGTCATTTTAT
1 CACATAAGGGCAAAATAGTCATTTTAC
*
128208 CACATAAGGGCAAAATCA-TCATTTTAA
1 CACATAAGGGCAAAAT-AGTCATTTTAC
* * * *
128235 AATATAAGGG-AAAGACAGTCATTTTGC
1 CACATAAGGGCAAA-ATAGTCATTTTAC
** *
128262 CACAT--GGTG-AAACCA-TCATTTTAT
1 CACATAAGG-GCAAAATAGTCATTTTAC
* *
128286 CACATACGGGCAAAATCA-TCATTTTAA
1 CACATAAGGGCAAAAT-AGTCATTTTAC
* *
128313 CACATAAGGG-AAAATCGTCATTTTAA
1 CACATAAGGGCAAAATAGTCATTTTAC
* *
128339 CATATAAGGGCAAAACAGTCATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTAC
128366 C
1 C
128367 CTATGGGAGA
Statistics
Matches: 314, Mismatches: 64, Indels: 44
0.74 0.15 0.10
Matches are distributed among these distances:
24 12 0.04
25 18 0.06
26 55 0.18
27 222 0.71
28 7 0.02
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (27 bp):
CACATAAGGGCAAAATAGTCATTTTAC
Found at i:128212 original size:81 final size:79
Alignment explanation
Indices: 127940--128364 Score: 337
Period size: 81 Copynumber: 5.3 Consensus size: 79
127930 AAACATACAT
* ** ** * * * * *
127940 CACATAGGGGCAAAATAGTCATCCTACCACATAAGGGAAAATTAGTCATTTTACCTCATAAGGGA
1 CACATAAGGGCAAAACCGTCATTTTAACACATAAGGCAAAATCA-TCATTTTAACACATAAGGGA
*
128005 AAA-ATTGTCATTTTAT
65 AAACA-T-TCATTTTAC
* * **
128021 CACATAAGGGCAAATCCGTCATTTTAACAC-CAAGGCAAAA-CAATCATTTTGCCACATAAGGGA
1 CACATAAGGGCAAAACCGTCATTTTAACACATAAGGCAAAATC-ATCATTTTAACACATAAGGGA
*
128084 AAA-ATTGTCATTTTAT
65 AAACA-T-TCATTTTAC
* * * * * *
128100 CACATAAGGGCAAAATCATTATGTTAACACATAAGGCAAAAACAGTCATTTTGACACATAAGGGT
1 CACATAAGGGCAAAACCGTCATTTTAACACATAAGGCAAAATCA-TCATTTTAACACATAAGGG-
*
128165 AAAACATTCATTTTGC
64 AAAACATTCATTTTAC
* * * * *
128181 CATATAAGGGAAAAACCGTCATTTTATCACATAAGGGCAAAATCATCATTTTAAAATATAAGGGA
1 CACATAAGGGCAAAACCGTCATTTTAACACATAA-GGCAAAATCATCATTTTAACACATAAGGGA
* *
128246 AAGACAGTCATTTTGC
65 AA-ACATTCATTTTAC
* * *
128262 CACAT--GGTG--AAACCATCATTTTATCACATACGGGCAAAATCATCATTTTAACACATAAGGG
1 CACATAAGG-GCAAAACCGTCATTTTAACACATA-AGGCAAAATCATCATTTTAACACATAAGGG
* *
128323 AAAATC-GTCATTTTAA
64 AAAA-CATTCATTTTAC
* *
128339 CATATAAGGGCAAAACAGTCATTTTA
1 CACATAAGGGCAAAACCGTCATTTTA
128365 CCCTATGGGA
Statistics
Matches: 286, Mismatches: 43, Indels: 31
0.79 0.12 0.09
Matches are distributed among these distances:
77 13 0.05
78 52 0.18
79 63 0.22
80 35 0.12
81 108 0.38
82 14 0.05
83 1 0.00
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (79 bp):
CACATAAGGGCAAAACCGTCATTTTAACACATAAGGCAAAATCATCATTTTAACACATAAGGGAA
AACATTCATTTTAC
Found at i:128812 original size:24 final size:24
Alignment explanation
Indices: 128780--128848 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
128770 CTACAACCCG
*
128780 CTTTTCGGCTTTTCAACCTTTCGA
1 CTTTTCGGCTTTTCAGCCTTTCGA
* *
128804 CTTTTCGGCTTTTCAGCCGTTCGG
1 CTTTTCGGCTTTTCAGCCTTTCGA
* *
128828 GTTTTCAGCTTTTCAGCCTTT
1 CTTTTCGGCTTTTCAGCCTTT
128849 GCAGTTTCAC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.09, C:0.28, G:0.17, T:0.46
Consensus pattern (24 bp):
CTTTTCGGCTTTTCAGCCTTTCGA
Found at i:131585 original size:18 final size:18
Alignment explanation
Indices: 131559--131633 Score: 62
Period size: 18 Copynumber: 4.1 Consensus size: 18
131549 CTTGGCCCAT
*
131559 TACAGTAACAGTAAACAG
1 TACAATAACAGTAAACAG
*
131577 TACAATAACACTAAACAG
1 TACAATAACAGTAAACAG
* ** * *
131595 TGCAGCAGCAGT-AACAT
1 TACAATAACAGTAAACAG
131612 TATGCAATAACAGTAAACAG
1 TA--CAATAACAGTAAACAG
131632 TA
1 TA
131634 TGCAAGTCCT
Statistics
Matches: 41, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
17 5 0.12
18 23 0.56
19 7 0.17
20 6 0.15
ACGTcount: A:0.48, C:0.19, G:0.15, T:0.19
Consensus pattern (18 bp):
TACAATAACAGTAAACAG
Found at i:131992 original size:27 final size:27
Alignment explanation
Indices: 131957--132410 Score: 334
Period size: 27 Copynumber: 17.0 Consensus size: 27
131947 AAACATACAT
* * **
131957 CACAT-AGGGGAAAAAAATCATCCTAC
1 CACATAAGGGCAAAAAAGTCATTTTAC
*
131983 CACATAAGGGCAAAATAGTCATTTTAC
1 CACATAAGGGCAAAAAAGTCATTTTAC
* *
132010 CTCATAAGGG-AAAAATTGTCATTTTAC
1 CACATAAGGGCAAAAA-AGTCATTTTAC
** *
132037 CACATAAGGGCAAAACCGTCATTTTAA
1 CACATAAGGGCAAAAAAGTCATTTTAC
* * *
132064 CACATAAGGGCAAAACATTCATTTTTC
1 CACATAAGGGCAAAAAAGTCATTTTAC
* * * * *
132091 CATAAAAAGGCAAAACTA-TCATTTTAT
1 CACATAAGGGCAAAA-AAGTCATTTTAC
* ** *
132118 CACATGAGGGCAAAATTGTCATTTTAA
1 CACATAAGGGCAAAAAAGTCATTTTAC
* *
132145 CACATAAGGGCAAAACAGCCATTTTGA-
1 CACATAAGGGCAAAAAAGTCATTTT-AC
* * *
132172 CAC--AAGCGCAAAACAGTCATTTTGC
1 CACATAAGGGCAAAAAAGTCATTTTAC
* ** *
132197 CCCATAAGGGCAAAACTGTCATTTTAT
1 CACATAAGGGCAAAAAAGTCATTTTAC
** * *
132224 CACATAAGGGCAAAATTGTAATTTTAA
1 CACATAAGGGCAAAAAAGTCATTTTAC
132251 CACATAAGGGCAAAAAAGTCATTTTGA-
1 CACATAAGGGCAAAAAAGTCATTTT-AC
* * *
132278 CACATAAGGGTAAAATAGTCATTTTGC
1 CACATAAGGGCAAAAAAGTCATTTTAC
* ** ** *
132305 CACAT-ACGATAAAACCGTCATTTTAT
1 CACATAAGGGCAAAAAAGTCATTTTAC
* *
132331 CACATAAGGGCAAAATAGTCATTTTAA
1 CACATAAGGGCAAAAAAGTCATTTTAC
** * *
132358 CACAT--GGGCAAAATTGTCACTTTAA
1 CACATAAGGGCAAAAAAGTCATTTTAC
* *
132383 CACATAAGGGTAAAATAGTCATTTTAC
1 CACATAAGGGCAAAAAAGTCATTTTAC
132410 C
1 C
132411 CTGTGGGGGA
Statistics
Matches: 346, Mismatches: 68, Indels: 27
0.78 0.15 0.06
Matches are distributed among these distances:
25 43 0.12
26 30 0.09
27 266 0.77
28 7 0.02
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (27 bp):
CACATAAGGGCAAAAAAGTCATTTTAC
Found at i:132038 original size:54 final size:54
Alignment explanation
Indices: 131980--132410 Score: 421
Period size: 54 Copynumber: 8.1 Consensus size: 54
131970 AAAATCATCC
* * * *
131980 TACCACATAAGGGCAAAATAGTCATTTTACCTCATAAGGGAAAAATTGTCATTT
1 TACCACATAAGGGCAAAATAGTCATTTTATCACATAAGGGCAAAATAGTCATTT
** * * *
132034 TACCACATAAGGGCAAAACCGTCATTTTAACACATAAGGGCAAAACATTCATTT
1 TACCACATAAGGGCAAAATAGTCATTTTATCACATAAGGGCAAAATAGTCATTT
* * * * * *
132088 TTCCATAAAAAGGCAAAACTA-TCATTTTATCACATGAGGGCAAAATTGTCATTT
1 TACCACATAAGGGCAAAA-TAGTCATTTTATCACATAAGGGCAAAATAGTCATTT
* * * * *
132142 TAACACATAAGGGCAAAACAGCCATTTTGA-CAC--AAGCGCAAAACAGTCATTT
1 TACCACATAAGGGCAAAATAGTCATTTT-ATCACATAAGGGCAAAATAGTCATTT
* * * *
132194 TGCCCCATAAGGGCAAAACT-GTCATTTTATCACATAAGGGCAAAATTGTAATTT
1 TACCACATAAGGGCAAAA-TAGTCATTTTATCACATAAGGGCAAAATAGTCATTT
* * *
132248 TAACACATAAGGGCAAAAAAGTCATTTTGA-CACATAAGGGTAAAATAGTCATTT
1 TACCACATAAGGGCAAAATAGTCATTTT-ATCACATAAGGGCAAAATAGTCATTT
* * ** **
132302 TGCCACAT-ACGATAAAACCGTCATTTTATCACATAAGGGCAAAATAGTCATTT
1 TACCACATAAGGGCAAAATAGTCATTTTATCACATAAGGGCAAAATAGTCATTT
* * * * *
132355 TAACACAT--GGGCAAAATTGTCACTTTAACACATAAGGGTAAAATAGTCATTT
1 TACCACATAAGGGCAAAATAGTCATTTTATCACATAAGGGCAAAATAGTCATTT
132407 TACC
1 TACC
132411 CTGTGGGGGA
Statistics
Matches: 302, Mismatches: 65, Indels: 22
0.78 0.17 0.06
Matches are distributed among these distances:
51 1 0.00
52 80 0.26
53 44 0.15
54 175 0.58
55 2 0.01
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.27
Consensus pattern (54 bp):
TACCACATAAGGGCAAAATAGTCATTTTATCACATAAGGGCAAAATAGTCATTT
Found at i:132086 original size:81 final size:81
Alignment explanation
Indices: 131983--132410 Score: 422
Period size: 81 Copynumber: 5.3 Consensus size: 81
131973 ATCATCCTAC
* * * **
131983 CACATAAGGGCAAAATAGTCATTTTACCTCATAAGGGAAAAATTGTCATTTTACCACATAAGGGC
1 CACATAAGGGCAAAACAGTCATTTTACCACATAAGGGCAAAACAGTCATTTTACCACATAAGGGC
**
132048 AAAACCGTCATTTTAA
66 AAAATTGTCATTTTAA
* * * * * * *
132064 CACATAAGGGCAAAACATTCATTTTTCCATAAAAAGGCAAAACTA-TCATTTTATCACATGAGGG
1 CACATAAGGGCAAAACAGTCATTTTACCACATAAGGGCAAAAC-AGTCATTTTACCACATAAGGG
132128 CAAAATTGTCATTTTAA
65 CAAAATTGTCATTTTAA
* * * *
132145 CACATAAGGGCAAAACAGCCATTTTGA-CAC--AAGCGCAAAACAGTCATTTTGCCCCATAAGGG
1 CACATAAGGGCAAAACAGTCATTTT-ACCACATAAGGGCAAAACAGTCATTTTACCACATAAGGG
* *
132207 CAAAACTGTCATTTTAT
65 CAAAATTGTCATTTTAA
** * * *
132224 CACATAAGGGCAAAATTGTAATTTTAACACATAAGGGCAAAAAAGTCATTTTGA-CACATAAGGG
1 CACATAAGGGCAAAACAGTCATTTTACCACATAAGGGCAAAACAGTCATTTT-ACCACATAAGGG
* * **
132288 TAAAATAGTCATTTTGC
65 CAAAATTGTCATTTTAA
* ** * * * *
132305 CACAT-ACGATAAAACCGTCATTTTATCACATAAGGGCAAAATAGTCATTTTAACACAT--GGGC
1 CACATAAGGGCAAAACAGTCATTTTACCACATAAGGGCAAAACAGTCATTTTACCACATAAGGGC
*
132367 AAAATTGTCACTTTAA
66 AAAATTGTCATTTTAA
* *
132383 CACATAAGGGTAAAATAGTCATTTTACC
1 CACATAAGGGCAAAACAGTCATTTTACC
132411 CTGTGGGGGA
Statistics
Matches: 281, Mismatches: 57, Indels: 20
0.78 0.16 0.06
Matches are distributed among these distances:
78 22 0.08
79 81 0.29
80 43 0.15
81 135 0.48
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (81 bp):
CACATAAGGGCAAAACAGTCATTTTACCACATAAGGGCAAAACAGTCATTTTACCACATAAGGGC
AAAATTGTCATTTTAA
Found at i:133020 original size:14 final size:14
Alignment explanation
Indices: 133003--133029 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
132993 TTAAACACCT
133003 TCTTATTAACACTC
1 TCTTATTAACACTC
133017 TCTTATTAACACT
1 TCTTATTAACACT
133030 TAATCCCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.26, G:0.00, T:0.44
Consensus pattern (14 bp):
TCTTATTAACACTC
Found at i:139136 original size:43 final size:43
Alignment explanation
Indices: 139075--139161 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
139065 TGATGGAGAA
139075 AACCTTATTTTCCTTGTGGAAAAGGTTAGAAACTTTTTATACG
1 AACCTTATTTTCCTTGTGGAAAAGGTTAGAAACTTTTTATACG
*
139118 AACCTTATTTTTCTTGTGGAAAAGGTTAGAAACTTTTTATACG
1 AACCTTATTTTCCTTGTGGAAAAGGTTAGAAACTTTTTATACG
139161 A
1 A
139162 TTAAGTCACA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (43 bp):
AACCTTATTTTCCTTGTGGAAAAGGTTAGAAACTTTTTATACG
Found at i:143696 original size:27 final size:27
Alignment explanation
Indices: 143659--143943 Score: 270
Period size: 27 Copynumber: 10.6 Consensus size: 27
143649 TTAGTTTACC
143659 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
* * * * *
143686 AATTTCTAAAATACCCTTGGTTTATAA
1 AATTACCAAAATACCCCTAGTTTGTAA
* **
143713 AATCACCAAAATACCTTTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
* * * *
143740 AATTACTAAAATACCCTTGGTTTATAA
1 AATTACCAAAATACCCCTAGTTTGTAA
* *
143767 AATTACC-AAATACCTCTAGTTTGTGA
1 AATTACCAAAATACCCCTAGTTTGTAA
143793 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
* *
143820 AATTATCAAAATACCTCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
* * *
143847 AATTACCAAAATACCCTTAATTTGTGA
1 AATTACCAAAATACCCCTAGTTTGTAA
** * *
143874 AATTACTGAAATA-CCCTCGACTTGTAA
1 AATTACCAAAATACCCCTAG-TTTGTAA
*** * *
143901 AATTATTGAAATA-CCCTCGACTTGTAA
1 AATTACCAAAATACCCCTAG-TTTGTAA
*
143928 AATTACCAAAGTACCC
1 AATTACCAAAATACCC
143944 TTGATTTACA
Statistics
Matches: 212, Mismatches: 43, Indels: 5
0.82 0.17 0.02
Matches are distributed among these distances:
26 24 0.11
27 186 0.88
28 2 0.01
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.33
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAGTTTGTAA
Found at i:143723 original size:54 final size:54
Alignment explanation
Indices: 143659--143864 Score: 306
Period size: 54 Copynumber: 3.8 Consensus size: 54
143649 TTAGTTTACC
* * *
143659 AATTACCAAAATACCCCTAGTTTGTAAAATTTCTAAAATACCCTTGGTTTATAA
1 AATTACCAAAATACCTCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTATAA
* * *
143713 AATCACCAAAATACCTTTAGTTTGTAAAATTACTAAAATACCCTTGGTTTATAA
1 AATTACCAAAATACCTCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTATAA
* * * *
143767 AATTACC-AAATACCTCTAGTTTGTGAAATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCTCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTATAA
*
143820 AATTATCAAAATACCTCTAGTTTGTAAAATTACCAAAATACCCTT
1 AATTACCAAAATACCTCTAGTTTGTAAAATTACCAAAATACCCTT
143865 AATTTGTGAA
Statistics
Matches: 137, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
53 46 0.34
54 91 0.66
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.34
Consensus pattern (54 bp):
AATTACCAAAATACCTCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTATAA
Found at i:143841 original size:107 final size:108
Alignment explanation
Indices: 143659--143864 Score: 306
Period size: 107 Copynumber: 1.9 Consensus size: 108
143649 TTAGTTTACC
* * * *
143659 AATTACCAAAATACCCCTAGTTTGTAAAATTTCTAAAATACCCTTGGTTTATAAAATCACCAAAA
1 AATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTAGTTTATAAAATCACCAAAA
* *
143724 TACCTTTAGTTTGTAAAATTACTAAAATACCCTTGGTTTATAA
66 TACCTCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTATAA
* * * * *
143767 AATTACC-AAATACCTCTAGTTTGTGAAATTACCAAAATACCCCTAGTTTGTAAAATTATCAAAA
1 AATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTAGTTTATAAAATCACCAAAA
143831 TACCTCTAGTTTGTAAAATTACCAAAATACCCTT
66 TACCTCTAGTTTGTAAAATTACCAAAATACCCTT
143865 AATTTGTGAA
Statistics
Matches: 87, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
107 80 0.92
108 7 0.08
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.34
Consensus pattern (108 bp):
AATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTAGTTTATAAAATCACCAAAA
TACCTCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTATAA
Found at i:143871 original size:54 final size:54
Alignment explanation
Indices: 143659--143905 Score: 300
Period size: 54 Copynumber: 4.6 Consensus size: 54
143649 TTAGTTTACC
* * * *
143659 AATTACCAAAATACCCCTAGTTTGTAAAATTTCTAAAATACCCTTGGTTTATAA
1 AATTACCAAAATACCTCTAGTTTGTAAAATTACCAAAATACCCTTAGTTTATAA
* * * *
143713 AATCACCAAAATACCTTTAGTTTGTAAAATTACTAAAATACCCTTGGTTTATAA
1 AATTACCAAAATACCTCTAGTTTGTAAAATTACCAAAATACCCTTAGTTTATAA
* * *
143767 AATTACC-AAATACCTCTAGTTTGTGAAATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCTCTAGTTTGTAAAATTACCAAAATACCCTTAGTTTATAA
* * * *
143820 AATTATCAAAATACCTCTAGTTTGTAAAATTACCAAAATACCCTTAATTTGTGA
1 AATTACCAAAATACCTCTAGTTTGTAAAATTACCAAAATACCCTTAGTTTATAA
** * *
143874 AATTACTGAAATACC-CTCGACTTGTAAAATTA
1 AATTACCAAAATACCTCTAG-TTTGTAAAATTA
143906 TTGAAATACC
Statistics
Matches: 170, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
53 49 0.29
54 121 0.71
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (54 bp):
AATTACCAAAATACCTCTAGTTTGTAAAATTACCAAAATACCCTTAGTTTATAA
Found at i:143877 original size:107 final size:107
Alignment explanation
Indices: 143659--143889 Score: 300
Period size: 107 Copynumber: 2.1 Consensus size: 107
143649 TTAGTTTACC
* * * *
143659 AATTACCAAAATACCCCTAGTTTGTAAAATTTCTAAAATACCCTTGGTTTATAAAATCACCAAAA
1 AATTACC-AAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTAGTTTATAAAATCACCAAAA
* * **
143724 TACCTTTAGTTTGTAAAATTACTAAAATACCCTTGGTTTATAA
65 TACCTCTAGTTTGTAAAATTACCAAAATACCCTTAATTTATAA
* * * * *
143767 AATTACCAAATACCTCTAGTTTGTGAAATTACCAAAATACCCCTAGTTTGTAAAATTATCAAAAT
1 AATTACCAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTAGTTTATAAAATCACCAAAAT
* *
143832 ACCTCTAGTTTGTAAAATTACCAAAATACCCTTAATTTGTGA
66 ACCTCTAGTTTGTAAAATTACCAAAATACCCTTAATTTATAA
*
143874 AATTACTGAAATACCC
1 AATTAC-CAAATACCC
143890 TCGACTTGTA
Statistics
Matches: 105, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
107 91 0.87
108 14 0.13
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.34
Consensus pattern (107 bp):
AATTACCAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTAGTTTATAAAATCACCAAAAT
ACCTCTAGTTTGTAAAATTACCAAAATACCCTTAATTTATAA
Found at i:143902 original size:134 final size:134
Alignment explanation
Indices: 143659--143905 Score: 363
Period size: 134 Copynumber: 1.8 Consensus size: 134
143649 TTAGTTTACC
*
143659 AATTACCAAAATACCCCTAGTTTGTAAAATTTCTAAAATACCCTTGGTTTATAAAATCACCAAAA
1 AATTACCAAAATACCCCTAGTTTGTAAAATTTCTAAAATACCCTTAGTTTATAAAATCACCAAAA
* * * **
143724 TACCTTTAGTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAATTACCAAATACCTCTAGTTT
66 TACCCTTAATTTGTAAAATTACTAAAATACCCTCGACTTATAAAATTACCAAATACCTCTAGTTT
143789 GTGA
131 GTGA
* *
143793 AATTACCAAAATACCCCTAGTTTGTAAAATTATC-AAAATA-CCTCTAGTTTGTAAAATTACCAA
1 AATTACCAAAATACCCCTAGTTTGTAAAATT-TCTAAAATACCCT-TAGTTTATAAAATCACCAA
* * *
143856 AATACCCTTAATTTGTGAAATTACTGAAATACCCTCGACTTGTAAAATTA
64 AATACCCTTAATTTGTAAAATTACTAAAATACCCTCGACTTATAAAATTA
143906 TTGAAATACC
Statistics
Matches: 100, Mismatches: 11, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
133 3 0.03
134 95 0.95
135 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (134 bp):
AATTACCAAAATACCCCTAGTTTGTAAAATTTCTAAAATACCCTTAGTTTATAAAATCACCAAAA
TACCCTTAATTTGTAAAATTACTAAAATACCCTCGACTTATAAAATTACCAAATACCTCTAGTTT
GTGA
Found at i:143959 original size:81 final size:82
Alignment explanation
Indices: 143814--143998 Score: 205
Period size: 81 Copynumber: 2.3 Consensus size: 82
143804 TACCCCTAGT
* * * **
143814 TTGTAAAATTATCAAAATA-CCTCTAGTTTGTAAAATTACCAAAATACCCTTAATTTGTGAAATT
1 TTGTAAAATTATCGAAATACCCTCGAGCTTGTAAAATTACCAAAATACCCTTAATTTCAGAAATT
143878 ACTGAAATACCCTCGAC
66 ACTGAAATACCCTCGAC
* * *
143895 TTGTAAAATTATTGAAATACCCTCGA-CTTGTAAAATTACCAAAGTACCCTTGATTTACAG-AAT
1 TTGTAAAATTATCGAAATACCCTCGAGCTTGTAAAATTACCAAAATACCCTTAATTT-CAGAAAT
* *** *
143958 TATTGTTTTACCCTCGAT
65 TACTGAAATACCCTCGAC
**
143976 TTACAAAATTATCGAAATACCCT
1 TTGTAAAATTATCGAAATACCCT
143999 TGTAGGGTAG
Statistics
Matches: 86, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
81 80 0.93
82 6 0.07
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (82 bp):
TTGTAAAATTATCGAAATACCCTCGAGCTTGTAAAATTACCAAAATACCCTTAATTTCAGAAATT
ACTGAAATACCCTCGAC
Found at i:143996 original size:27 final size:27
Alignment explanation
Indices: 143873--143998 Score: 94
Period size: 27 Copynumber: 4.7 Consensus size: 27
143863 TTAATTTGTG
**
143873 AAATTA-CTGAAATACCCTCGACTTGTA
1 AAATTATC-GAAATACCCTCGACTTACA
* **
143900 AAATTATTGAAATACCCTCGACTTGTA
1 AAATTATCGAAATACCCTCGACTTACA
* * *
143927 AAATTA-CCAAAGTACCCTTGATTTACA
1 AAATTATCGAAA-TACCCTCGACTTACA
* * *** *
143954 GAATTATTGTTTTACCCTCGATTTACA
1 AAATTATCGAAATACCCTCGACTTACA
143981 AAATTATCGAAATACCCT
1 AAATTATCGAAATACCCT
143999 TGTAGGGTAG
Statistics
Matches: 77, Mismatches: 19, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
26 3 0.04
27 74 0.96
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.33
Consensus pattern (27 bp):
AAATTATCGAAATACCCTCGACTTACA
Found at i:144017 original size:27 final size:27
Alignment explanation
Indices: 143985--144213 Score: 230
Period size: 27 Copynumber: 8.5 Consensus size: 27
143975 TTTACAAAAT
*
143985 TATCGAAATACCCTTGTAGGGTAGAAA
1 TATCGAAATACCCCTGTAGGGTAGAAA
* *
144012 TGTCGAAATACCCTTGTAGGGTAGAAA
1 TATCGAAATACCCCTGTAGGGTAGAAA
* *
144039 TACCGAAATACCCCTGTAAGGTAGAAA
1 TATCGAAATACCCCTGTAGGGTAGAAA
* * *
144066 TACCAAAATACCCCTGTAGGGTAGAAT
1 TATCGAAATACCCCTGTAGGGTAGAAA
* * *
144093 TA-CTAAAATACCCCTATAGGGTAGAAT
1 TATC-GAAATACCCCTGTAGGGTAGAAA
* * *
144120 TACCGAAATACCCTTGTAGGGTTGAAA
1 TATCGAAATACCCCTGTAGGGTAGAAA
144147 TATCGAAATACCCCTGTAGGGTA-AAA
1 TATCGAAATACCCCTGTAGGGTAGAAA
* * * * *
144173 T-TACTGAAGTACTCCTATAAGGTAGAAT
1 TAT-C-GAAATACCCCTGTAGGGTAGAAA
*
144201 TATCGAGATACCC
1 TATCGAAATACCC
144214 TTTTGGGGTA
Statistics
Matches: 171, Mismatches: 25, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
25 1 0.01
26 6 0.04
27 158 0.92
28 5 0.03
29 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.25
Consensus pattern (27 bp):
TATCGAAATACCCCTGTAGGGTAGAAA
Found at i:144214 original size:81 final size:80
Alignment explanation
Indices: 143985--144215 Score: 277
Period size: 81 Copynumber: 2.9 Consensus size: 80
143975 TTTACAAAAT
* * *
143985 TATCGAAATACCCTTGTAGGGTAGAAATGT-C-GAAATACCCTTGTAGGGTAGAAATACCGAAAT
1 TATCGAAATACCCCTGTAGGGTA-AAAT-TACTGAAATACCC-TATAGGGTAGAATTACCGAAAT
*
144048 ACCCCTGTAAGGTAGAAA
63 ACCCTTGTAAGGTAGAAA
* * * *
144066 TACCAAAATACCCCTGTAGGGTAGAATTACTAAAATACCCCTATAGGGTAGAATTACCGAAATAC
1 TATCGAAATACCCCTGTAGGGTAAAATTACTGAAATA-CCCTATAGGGTAGAATTACCGAAATAC
* *
144131 CCTTGTAGGGTTGAAA
65 CCTTGTAAGGTAGAAA
* * * *
144147 TATCGAAATACCCCTGTAGGGTAAAATTACTGAAGTACTCCTATAAGGTAGAATTATCGAGATAC
1 TATCGAAATACCCCTGTAGGGTAAAATTACTGAAATAC-CCTATAGGGTAGAATTACCGAAATAC
144212 CCTT
65 CCTT
144216 TTGGGGTAAA
Statistics
Matches: 128, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
79 1 0.01
80 5 0.04
81 119 0.93
82 3 0.02
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (80 bp):
TATCGAAATACCCCTGTAGGGTAAAATTACTGAAATACCCTATAGGGTAGAATTACCGAAATACC
CTTGTAAGGTAGAAA
Found at i:144620 original size:27 final size:26
Alignment explanation
Indices: 144568--144627 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
144558 ATATATATAT
*
144568 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
144594 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
144621 ATATCTG
1 ATATCTG
144628 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:144763 original size:6 final size:6
Alignment explanation
Indices: 144746--144907 Score: 95
Period size: 6 Copynumber: 26.3 Consensus size: 6
144736 TTCTATTCAC
* *
144746 ATTCTA ATTCTG ATTCTG -TTACCTG -TTACTG ATTCTG ATTCTG GTTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATT-CTG ATTCTG ATTCTG ATTCTG
* * * *
144795 ATTCTA ATTCTG -TTACCTA ATACTG ATTCTG ATTCTG -TTACCTA ATTCTG
1 ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG
* * *
144845 ATTCTA ATTCTG ATTTTG ATTCTG -TCACCTG ATTCT- AGTTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG A-TTCTG ATTCTG
144894 ATTCT- AGTTCTG AT
1 ATTCTG A-TTCTG AT
144908 AATGTTTCTT
Statistics
Matches: 122, Mismatches: 18, Indels: 32
0.71 0.10 0.19
Matches are distributed among these distances:
5 9 0.07
6 93 0.76
7 16 0.13
8 4 0.03
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:144780 original size:25 final size:24
Alignment explanation
Indices: 144746--144856 Score: 99
Period size: 25 Copynumber: 4.8 Consensus size: 24
144736 TTCTATTCAC
*
144746 ATTCTAATTCTGATTCTGTTACCT
1 ATTCTGATTCTGATTCTGTTACCT
*
144770 GTTACTGATTCTGATTCTG------
1 ATT-CTGATTCTGATTCTGTTACCT
* *
144789 GTTCTGATTCTAATTCTGTTACCT
1 ATTCTGATTCTGATTCTGTTACCT
*
144813 AATACTGATTCTGATTCTGTTACCT
1 -ATTCTGATTCTGATTCTGTTACCT
*
144838 AATTCTGATTCTAATTCTG
1 -ATTCTGATTCTGATTCTG
144857 ATTTTGATTC
Statistics
Matches: 71, Mismatches: 8, Indels: 15
0.76 0.09 0.16
Matches are distributed among these distances:
18 14 0.20
19 3 0.04
24 2 0.03
25 52 0.73
ACGTcount: A:0.21, C:0.19, G:0.13, T:0.48
Consensus pattern (24 bp):
ATTCTGATTCTGATTCTGTTACCT
Found at i:144819 original size:43 final size:43
Alignment explanation
Indices: 144747--144849 Score: 136
Period size: 43 Copynumber: 2.4 Consensus size: 43
144737 TCTATTCACA
* **
144747 TTCTAATTCTGATTCTGTTACCTGTTACTGATTCTGATTCTGG
1 TTCTAATTCTAATTCTGTTACCTAATACTGATTCTGATTCTGG
*
144790 TTCTGATTCTAATTCTGTTACCTAATACTGATTCTGATTCT-G
1 TTCTAATTCTAATTCTGTTACCTAATACTGATTCTGATTCTGG
*
144832 TTACCTAATTCTGATTCT
1 TT--CTAATTCTAATTCT
144850 AATTCTGATT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
42 3 0.06
43 37 0.71
44 12 0.23
ACGTcount: A:0.19, C:0.19, G:0.13, T:0.49
Consensus pattern (43 bp):
TTCTAATTCTAATTCTGTTACCTAATACTGATTCTGATTCTGG
Found at i:144905 original size:37 final size:37
Alignment explanation
Indices: 144811--144898 Score: 115
Period size: 37 Copynumber: 2.4 Consensus size: 37
144801 ATTCTGTTAC
* *
144811 CTAATACTGATTCTGATTCTGTTACCTAATTCTGATT
1 CTAATTCTGATTCTGATTCTGTCACCTAATTCTGATT
* *
144848 CTAATTCTGATTTTGATTCTGTCACCTGATTCT-AGTT
1 CTAATTCTGATTCTGATTCTGTCACCTAATTCTGA-TT
*
144885 CTGATTCTGATTCT
1 CTAATTCTGATTCT
144899 AGTTCTGATA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
36 1 0.02
37 43 0.98
ACGTcount: A:0.20, C:0.19, G:0.12, T:0.48
Consensus pattern (37 bp):
CTAATTCTGATTCTGATTCTGTCACCTAATTCTGATT
Found at i:144916 original size:18 final size:18
Alignment explanation
Indices: 144874--144928 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
144864 TTCTGTCACC
**
144874 TGATTCTAGTTCTGATTC
1 TGATTCTAGTTCTGATAA
144892 TGATTCTAGTTCTGATAA
1 TGATTCTAGTTCTGATAA
*
144910 TGTTTCTTA-TTCTG-TAA
1 TGATTC-TAGTTCTGATAA
144927 TG
1 TG
144929 GGTTAAAGCC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 5 0.15
18 26 0.79
19 2 0.06
ACGTcount: A:0.20, C:0.13, G:0.16, T:0.51
Consensus pattern (18 bp):
TGATTCTAGTTCTGATAA
Found at i:147795 original size:28 final size:28
Alignment explanation
Indices: 147763--147827 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
147753 ATTTACTAGA
*
147763 ATACCCCTATGTATACAAAATTACCATT
1 ATACCCCTATGTATACAAAATGACCATT
* *
147791 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATACAAAATGACCATT
147819 ATACCCCTA
1 ATACCCCTA
147828 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.35, C:0.28, G:0.06, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATACAAAATGACCATT
Found at i:147974 original size:28 final size:27
Alignment explanation
Indices: 147933--148022 Score: 101
Period size: 27 Copynumber: 3.2 Consensus size: 27
147923 AGGAAGCGTC
147933 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* **
147961 CTGGTGGCCCTGCCACGTATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
*
147988 CTGGTGGCACTGCCACAAAATATCAGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
148017 CTGGTG
1 CTGGTG
148023 ACTCTGTCTC
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 23 0.44
28 22 0.42
29 7 0.13
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.31
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:148510 original size:19 final size:19
Alignment explanation
Indices: 148486--148524 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
148476 TTTTAATTAT
* *
148486 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
148505 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
148524 T
1 T
148525 ATGATGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Done.