Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014361.1 Kokia drynarioides strain JFW-HI SEQ_129398, 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: 142714
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Warning! 16 characters in sequence are not A, C, G, or T
Found at i:1629 original size:31 final size:30
Alignment explanation
Indices: 1533--1631 Score: 92
Period size: 31 Copynumber: 3.1 Consensus size: 30
1523 ACGTTTTGGG
* * *
1533 AAATTTTGAGAGGATTAATTAGAATTTCCAA
1 AAATTTTG-GAAGATTAATTAAAATTTCTAA
1564 AAATTTTGGAAGATCTAATTTTAAAAATTT-TAA
1 AAATTTTGGAAGAT-TAA--TT-AAAATTTCTAA
* *
1597 AACTTTTGGAAGGCTTAATTAAAATTTCTAA
1 AAATTTTGGAA-GATTAATTAAAATTTCTAA
1628 AAAT
1 AAAT
1632 CTTAGGGGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
30 12 0.21
31 19 0.34
33 17 0.30
34 8 0.14
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.38
Consensus pattern (30 bp):
AAATTTTGGAAGATTAATTAAAATTTCTAA
Found at i:7485 original size:12 final size:12
Alignment explanation
Indices: 7468--7492 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
7458 GAACTTGAAC
7468 ATTCAAGGCCCA
1 ATTCAAGGCCCA
7480 ATTCAAGGCCCA
1 ATTCAAGGCCCA
7492 A
1 A
7493 GTTTGGTCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.32, G:0.16, T:0.16
Consensus pattern (12 bp):
ATTCAAGGCCCA
Found at i:10028 original size:15 final size:15
Alignment explanation
Indices: 10008--10069 Score: 60
Period size: 13 Copynumber: 4.4 Consensus size: 15
9998 ACTCTACTTT
*
10008 TATAATGTTATATTA
1 TATAATGTAATATTA
*
10023 TATAAT-TAAT-TTT
1 TATAATGTAATATTA
*
10036 TATAATGTGATATTA
1 TATAATGTAATATTA
10051 TATAAT-TAAT-TTA
1 TATAATGTAATATTA
*
10064 AATAAT
1 TATAAT
10070 TAACGTATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 16 0.41
14 9 0.23
15 14 0.36
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.52
Consensus pattern (15 bp):
TATAATGTAATATTA
Found at i:10037 original size:28 final size:28
Alignment explanation
Indices: 10005--10062 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
9995 GATACTCTAC
*
10005 TTTTATAATGTTATATTATATAATTAAT
1 TTTTATAATGTGATATTATATAATTAAT
10033 TTTTATAATGTGATATTATATAATTAAT
1 TTTTATAATGTGATATTATATAATTAAT
10061 TT
1 TT
10063 AAATAATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (28 bp):
TTTTATAATGTGATATTATATAATTAAT
Found at i:10039 original size:13 final size:13
Alignment explanation
Indices: 10020--10072 Score: 61
Period size: 13 Copynumber: 3.9 Consensus size: 13
10010 TAATGTTATA
10020 TTATATAATTAAT
1 TTATATAATTAAT
* *
10033 TTTTATAATGTGAT
1 TTATATAAT-TAAT
10047 ATTATATAATTAAT
1 -TTATATAATTAAT
*
10061 TTAAATAATTAA
1 TTATATAATTAA
10073 CGTATAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
13 19 0.58
14 6 0.18
15 8 0.24
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (13 bp):
TTATATAATTAAT
Found at i:10068 original size:28 final size:28
Alignment explanation
Indices: 10009--10069 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
9999 CTCTACTTTT
* **
10009 ATAATGTTATATTATATAATTAATTTTT
1 ATAATGTGATATTATATAATTAATTTAA
10037 ATAATGTGATATTATATAATTAATTTAA
1 ATAATGTGATATTATATAATTAATTTAA
10065 ATAAT
1 ATAAT
10070 TAACGTATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (28 bp):
ATAATGTGATATTATATAATTAATTTAA
Found at i:10902 original size:3 final size:3
Alignment explanation
Indices: 10894--10922 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
10884 GGCGAAGTTG
10894 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
10923 TTAATATACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12958 original size:73 final size:73
Alignment explanation
Indices: 12871--13015 Score: 263
Period size: 73 Copynumber: 2.0 Consensus size: 73
12861 TTTTAGAGGG
* * *
12871 ACTAATTTGTTCAATTTCAAAATTGAGAAAGATTGAAGATGTCATTTTAGCTTTTATGTATATAT
1 ACTAATTTGTTCAATTTCAAAATTGAAAAAGATTGAAGATGTCATTTTAGCTTATATATATATAT
12936 ATATATAC
66 ATATATAC
12944 ACTAATTTGTTCAATTTCAAAATTGAAAAAGATTGAAGATGTCATTTTAGCTTATATATATATAT
1 ACTAATTTGTTCAATTTCAAAATTGAAAAAGATTGAAGATGTCATTTTAGCTTATATATATATAT
13009 ATATATA
66 ATATATA
13016 TATATATGTG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (73 bp):
ACTAATTTGTTCAATTTCAAAATTGAAAAAGATTGAAGATGTCATTTTAGCTTATATATATATAT
ATATATAC
Found at i:13003 original size:2 final size:2
Alignment explanation
Indices: 12996--13022 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12986 CATTTTAGCT
12996 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
13023 GTGTGTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14446 original size:26 final size:27
Alignment explanation
Indices: 14417--14477 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 27
14407 AAAATGAGAC
*
14417 TTTTGGATAC-GGGGGTAAAATGGTAA
1 TTTTGGATACTGGGGGCAAAATGGTAA
* *
14443 TTTTGGATGCTTGGGGGCGAAATGGTAA
1 TTTTGGATAC-TGGGGGCAAAATGGTAA
14471 TTTTGGA
1 TTTTGGA
14478 AGGCTCGAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 9 0.30
28 21 0.70
ACGTcount: A:0.25, C:0.05, G:0.36, T:0.34
Consensus pattern (27 bp):
TTTTGGATACTGGGGGCAAAATGGTAA
Found at i:14522 original size:29 final size:28
Alignment explanation
Indices: 14491--14595 Score: 81
Period size: 29 Copynumber: 3.6 Consensus size: 28
14481 CTCGAGGTCA
*
14491 AAAATGG-AGTTTTTGGACATTTGAGGGT
1 AAAATGGTAATTTTTGGACATTTG-GGGT
*
14519 AAAATGGTAATTTTTGGA-AGGTTGGGGAT
1 AAAATGGTAATTTTTGGACA-TTTGGGG-T
* * **
14548 AAAAAATGG-AGTTTTTAGACATCCGGGGGT
1 --AAAATGGTAATTTTTGGACAT-TTGGGGT
14578 AAAATGGTAATTTTTGGA
1 AAAATGGTAATTTTTGGA
14596 AGGTTTCGGT
Statistics
Matches: 60, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
28 18 0.30
29 21 0.35
30 9 0.15
31 12 0.20
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.33
Consensus pattern (28 bp):
AAAATGGTAATTTTTGGACATTTGGGGT
Found at i:14563 original size:59 final size:59
Alignment explanation
Indices: 14462--15004 Score: 518
Period size: 59 Copynumber: 9.3 Consensus size: 59
14452 CTTGGGGGCG
* * * *
14462 AAATGGTAA-TTTTGGAAGGCTCGAGG-TCAAAAATGGAGTTTTTGGACATTTGAGGGTA
1 AAATGGTAATTTTTGGAAGGTTCG-GGATCAAAAATGGAGTTTTTAGACATTCGGGGGTA
* * *
14520 AAATGGTAATTTTTGGAAGGTTGGGGATAAAAAATGGAGTTTTTAGACATCCGGGGGTA
1 AAATGGTAATTTTTGGAAGGTTCGGGATCAAAAATGGAGTTTTTAGACATTCGGGGGTA
* * *
14579 AAATGGTAATTTTTGGAAGGTTTC-GG-TAAAAAATGGAGTATTTAAACATTCGGGGGTA
1 AAATGGTAATTTTTGGAAGG-TTCGGGATCAAAAATGGAGTTTTTAGACATTCGGGGGTA
* * * *
14637 AAATGGTAATTTTTGGAAGGTTTC--GATAAAAAATGGAGTATTTAAACATCCGGGGGTA
1 AAATGGTAATTTTTGGAAGG-TTCGGGATCAAAAATGGAGTTTTTAGACATTCGGGGGTA
* * *** *
14695 AAATGGTAAATTTTGGAAGGTTCGAGATCAAAAACAAAGTTTTTAGACATTTGGGGGTA
1 AAATGGTAATTTTTGGAAGGTTCGGGATCAAAAATGGAGTTTTTAGACATTCGGGGGTA
*** * * * * *
14754 AAAAAATAATTTTTGGAAGTTTC-GAAGTCAAAAATAGGA-TTTTTGGA-AGTTCAGAGGTA
1 AAATGGTAATTTTTGGAAGGTTCGGGA-TCAAAAAT-GGAGTTTTTAGACA-TTCGGGGGTA
* *
14813 AAATGGTAA-TTTTGGAATGTTCGAGAT-AAAAATGGAGTTTTTAGACATTCGGGGGTA
1 AAATGGTAATTTTTGGAAGGTTCGGGATCAAAAATGGAGTTTTTAGACATTCGGGGGTA
* * * * * * * * *
14870 AAATTGTAAATTTTGGAAGGTTCAGGATTAGAAACGGAGTTTTTAAACATCCAGGGGTA
1 AAATGGTAATTTTTGGAAGGTTCGGGATCAAAAATGGAGTTTTTAGACATTCGGGGGTA
* * * * * * *
14929 AAATGGTAATTTTTGAAAGTTTCGGGTTCAAAAATGGA-ATTTTGGAAAGTTCAGGGGTA
1 AAATGGTAATTTTTGGAAGGTTCGGGATCAAAAATGGAGTTTTTAGACA-TTCGGGGGTA
14988 AAAT-GTAATTTTTGGAA
1 AAATGGTAATTTTTGGAA
15005 AAATCAAGGT
Statistics
Matches: 401, Mismatches: 69, Indels: 30
0.80 0.14 0.06
Matches are distributed among these distances:
56 3 0.01
57 33 0.08
58 162 0.40
59 200 0.50
60 3 0.01
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (59 bp):
AAATGGTAATTTTTGGAAGGTTCGGGATCAAAAATGGAGTTTTTAGACATTCGGGGGTA
Found at i:14614 original size:30 final size:30
Alignment explanation
Indices: 14578--14672 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 30
14568 ATCCGGGGGT
14578 AAAATGGTAATTTTTGGAAGGTTTCGGTAA
1 AAAATGGTAATTTTTGGAAGGTTTCGGTAA
* * *** ***
14608 AAAATGG-AGTATTT--AAACATTCGGGGGT
1 AAAATGGTAATTTTTGGAAGGTTTC-GGTAA
*
14636 AAAATGGTAATTTTTGGAAGGTTTCGATAA
1 AAAATGGTAATTTTTGGAAGGTTTCGGTAA
14666 AAAATGG
1 AAAATGG
14673 AGTATTTAAA
Statistics
Matches: 44, Mismatches: 17, Indels: 8
0.64 0.25 0.12
Matches are distributed among these distances:
27 5 0.11
28 9 0.20
29 10 0.23
30 15 0.34
31 5 0.11
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.33
Consensus pattern (30 bp):
AAAATGGTAATTTTTGGAAGGTTTCGGTAA
Found at i:14738 original size:175 final size:170
Alignment explanation
Indices: 14462--15004 Score: 597
Period size: 175 Copynumber: 3.1 Consensus size: 170
14452 CTTGGGGGCG
* * * * *
14462 AAATGGTAATTTTGGAAGGCTCGAGGTCAAAAATGGAGTTTTTGGACATTTGAGGGTAAAATGGT
1 AAATGGTAATTTTGGAAGGTTCGA--TAAAAAATGGAGTTTTTAGACATTCGGGGGTAAAATGGT
* * * *
14527 AATTTTTGGAAGGTTGGGGATAAAAAATGGAGTTTTTAGACATCCGGGGGTAAAATGGTAATTTT
64 AAATTTTGGAAGGTTCGAGATAAAAAACGGAGTTTTTAGACATCCGGGGGTAAAATGGTAATTTT
* * *
14592 TGGAAGGTTTCGGTAAAAAATGGAGTATTT-AAACATTCGGGGGTA
129 TGGAA-GTTTCGGTCAAAAATGGA-T-TTTGAAA-GTTCAGGGGTA
* * *
14637 AAATGGTAATTTTTGGAAGGTTTCGATAAAAAATGGAGTATTTAAACATCCGGGGGTAAAATGGT
1 AAATGGTAA-TTTTGGAAGG-TTCGATAAAAAATGGAGTTTTTAGACATTCGGGGGTAAAATGGT
* ** ** ***
14702 AAATTTTGGAAGGTTCGAGATCAAAAACAAAGTTTTTAGACATTTGGGGGTAAAAAAATAATTTT
64 AAATTTTGGAAGGTTCGAGATAAAAAACGGAGTTTTTAGACATCCGGGGGTAAAATGGTAATTTT
* *
14767 TGGAAGTTTCGAAGTCAAAAATAGGATTTTTGGAAGTTCAGAGGTA
129 TGGAAGTTTCG--GTCAAAAAT-GGA-TTTTGAAAGTTCAGGGGTA
* * *
14813 AAATGGTAATTTTGGAATGTTCGAGATAAAAATGGAGTTTTTAGACATTCGGGGGTAAAATTGTA
1 AAATGGTAATTTTGGAAGGTTCGATA-AAAAATGGAGTTTTTAGACATTCGGGGGTAAAATGGTA
* * * *
14878 AATTTTGGAAGGTTC-AGGATTAGAAACGGAGTTTTTAAACATCCAGGGGTAAAATGGTAATTTT
65 AATTTTGGAAGGTTCGA-GATAAAAAACGGAGTTTTTAGACATCCGGGGGTAAAATGGTAATTTT
*
14942 TGAAAGTTTCGGGTTCAAAAATGGAATTTTGGAAAGTTCAGGGGTA
129 TGGAAGTTTC-GG-TCAAAAATGG-ATTTT-GAAAGTTCAGGGGTA
14988 AAAT-GTAATTTTTGGAA
1 AAATGGTAA-TTTTGGAA
15005 AAATCAAGGT
Statistics
Matches: 309, Mismatches: 46, Indels: 26
0.81 0.12 0.07
Matches are distributed among these distances:
174 24 0.08
175 236 0.76
176 39 0.13
177 10 0.03
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (170 bp):
AAATGGTAATTTTGGAAGGTTCGATAAAAAATGGAGTTTTTAGACATTCGGGGGTAAAATGGTAA
ATTTTGGAAGGTTCGAGATAAAAAACGGAGTTTTTAGACATCCGGGGGTAAAATGGTAATTTTTG
GAAGTTTCGGTCAAAAATGGATTTTGAAAGTTCAGGGGTA
Found at i:14815 original size:29 final size:27
Alignment explanation
Indices: 14762--14854 Score: 89
Period size: 28 Copynumber: 3.2 Consensus size: 27
14752 TAAAAAAATA
*
14762 ATTTTTGGAAGTTTCGAAGTCAAAAATAGG
1 ATTTTTGGAAG-TTCGAGGT-AAAAAT-GG
14792 ATTTTTGGAAGTTCAGAGGT-AAAATGG
1 ATTTTTGGAAGTTC-GAGGTAAAAATGG
* *
14819 TAATTTTGGAATGTTCGAGATAAAAATGG
1 -ATTTTTGGAA-GTTCGAGGTAAAAATGG
14848 AGTTTTT
1 A-TTTTT
14855 AGACATTCGG
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
27 2 0.04
28 19 0.35
29 18 0.33
30 15 0.28
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (27 bp):
ATTTTTGGAAGTTCGAGGTAAAAATGG
Found at i:14990 original size:29 final size:29
Alignment explanation
Indices: 14783--15031 Score: 111
Period size: 29 Copynumber: 8.6 Consensus size: 29
14773 TTTCGAAGTC
* *
14783 AAAAATAGGATTTTTGG-AAGTTCAGAGGT
1 AAAAAT-GGAATTTTGGAAAGTTCAGGGGT
* * *
14812 -AAAATGGTAATTTTGGAATGTTC-GAGAT
1 AAAAATGG-AATTTTGGAAAGTTCAGGGGT
* * * *
14840 AAAAATGGAGTTTTTAGACA-TTCGGGGGT
1 AAAAATGGA-ATTTTGGAAAGTTCAGGGGT
* * * **
14869 AAAATTGTAAATTTTGGAAGGTTCAGGATT
1 AAAAATG-GAATTTTGGAAAGTTCAGGGGT
* * * * * *
14899 AGAAACGGAGTTTT-TAAACATCCAGGGGT
1 AAAAATGGAATTTTGGAAA-GTTCAGGGGT
* *
14928 -AAAATGGTAATTTTTGAAAGTTTC-GGGTT
1 AAAAATGG-AATTTTGGAAAG-TTCAGGGGT
14957 CAAAAATGGAATTTTGGAAAGTTCAGGGGT
1 -AAAAATGGAATTTTGGAAAGTTCAGGGGT
* ** *
14987 -AAAATGTAATTTTTGGAAAAATCA-AGGT
1 AAAAATGGAA-TTTTGGAAAGTTCAGGGGT
*
15015 TAAAATGGAATTTTGGA
1 AAAAATGGAATTTTGGA
15032 GAACTTTGGG
Statistics
Matches: 161, Mismatches: 43, Indels: 33
0.68 0.18 0.14
Matches are distributed among these distances:
27 2 0.01
28 45 0.28
29 76 0.47
30 31 0.19
31 7 0.04
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.33
Consensus pattern (29 bp):
AAAAATGGAATTTTGGAAAGTTCAGGGGT
Found at i:16157 original size:19 final size:19
Alignment explanation
Indices: 16130--16177 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
16120 TTATTATTTG
* *
16130 TTTAATATTACCAAAAAAA
1 TTTATTATTACAAAAAAAA
**
16149 TTTATTATTTTAAAAAAAA
1 TTTATTATTACAAAAAAAA
16168 TTTATTATTA
1 TTTATTATTA
16178 TTATTATTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTATTATTACAAAAAAAA
Found at i:16175 original size:3 final size:3
Alignment explanation
Indices: 16169--16198 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
16159 TAAAAAAAAT
16169 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16199 CTAATAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:16923 original size:17 final size:17
Alignment explanation
Indices: 16898--16968 Score: 88
Period size: 17 Copynumber: 4.2 Consensus size: 17
16888 TTTTAATTTT
*
16898 ATTTTAATTTAAAATAA
1 ATTTGAATTTAAAATAA
16915 ATTTGAATTTAAAATAA
1 ATTTGAATTTAAAATAA
** * * *
16932 ATTCAAACTCAAAATGA
1 ATTTGAATTTAAAATAA
16949 ATTTGAATTTAAAATAA
1 ATTTGAATTTAAAATAA
16966 ATT
1 ATT
16969 CAAACTTATT
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 43 1.00
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (17 bp):
ATTTGAATTTAAAATAA
Found at i:16946 original size:34 final size:34
Alignment explanation
Indices: 16908--16974 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
16898 ATTTTAATTT
16908 AAAATAAATTTGAATTTAAAATAAATTCAAACTC
1 AAAATAAATTTGAATTTAAAATAAATTCAAACTC
*
16942 AAAATGAATTTGAATTTAAAATAAATTCAAACT
1 AAAATAAATTTGAATTTAAAATAAATTCAAACT
16975 TATTTAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.33
Consensus pattern (34 bp):
AAAATAAATTTGAATTTAAAATAAATTCAAACTC
Found at i:17399 original size:18 final size:18
Alignment explanation
Indices: 17376--17418 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
17366 TTTGCAGTTG
17376 TAATTAATTTAAAGTT-TT
1 TAATTAA-TTAAAGTTATT
*
17394 TAATTAATTAAATTTATT
1 TAATTAATTAAAGTTATT
17412 TAATTAA
1 TAATTAA
17419 AAATTTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAGTTATT
Found at i:17922 original size:182 final size:182
Alignment explanation
Indices: 17615--17979 Score: 730
Period size: 182 Copynumber: 2.0 Consensus size: 182
17605 AAATAAAATT
17615 GACTATTTTTATAGTTTACCTAAAAATAAATTGGATCTATTCAATCAGAATTTGAATTAGCTAAA
1 GACTATTTTTATAGTTTACCTAAAAATAAATTGGATCTATTCAATCAGAATTTGAATTAGCTAAA
17680 TTTAAATCTAATTTAATTGACTTAAACACGAAATAATCAAAAATTCAAAATGATCTAACTTGAAA
66 TTTAAATCTAATTTAATTGACTTAAACACGAAATAATCAAAAATTCAAAATGATCTAACTTGAAA
17745 ATTAAAGAAGTGTCCCGTCAAATTCCAACAGTTAAGTTTCAATTCATGAATA
131 ATTAAAGAAGTGTCCCGTCAAATTCCAACAGTTAAGTTTCAATTCATGAATA
17797 GACTATTTTTATAGTTTACCTAAAAATAAATTGGATCTATTCAATCAGAATTTGAATTAGCTAAA
1 GACTATTTTTATAGTTTACCTAAAAATAAATTGGATCTATTCAATCAGAATTTGAATTAGCTAAA
17862 TTTAAATCTAATTTAATTGACTTAAACACGAAATAATCAAAAATTCAAAATGATCTAACTTGAAA
66 TTTAAATCTAATTTAATTGACTTAAACACGAAATAATCAAAAATTCAAAATGATCTAACTTGAAA
17927 ATTAAAGAAGTGTCCCGTCAAATTCCAACAGTTAAGTTTCAATTCATGAATA
131 ATTAAAGAAGTGTCCCGTCAAATTCCAACAGTTAAGTTTCAATTCATGAATA
17979 G
1 G
17980 GGAAAACAAT
Statistics
Matches: 183, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
182 183 1.00
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (182 bp):
GACTATTTTTATAGTTTACCTAAAAATAAATTGGATCTATTCAATCAGAATTTGAATTAGCTAAA
TTTAAATCTAATTTAATTGACTTAAACACGAAATAATCAAAAATTCAAAATGATCTAACTTGAAA
ATTAAAGAAGTGTCCCGTCAAATTCCAACAGTTAAGTTTCAATTCATGAATA
Found at i:25445 original size:11 final size:12
Alignment explanation
Indices: 25402--25447 Score: 53
Period size: 11 Copynumber: 4.0 Consensus size: 12
25392 ATAAAATTAT
25402 TAAATATTAAAA
1 TAAATATTAAAA
*
25414 T-AATA-TAATA
1 TAAATATTAAAA
25424 TAAATATTTAAAA
1 TAAATA-TTAAAA
25437 TAAA-ATTAAAA
1 TAAATATTAAAA
25448 ATAATATGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
10 5 0.17
11 14 0.48
12 2 0.07
13 8 0.28
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
TAAATATTAAAA
Found at i:28099 original size:82 final size:82
Alignment explanation
Indices: 27991--28154 Score: 188
Period size: 81 Copynumber: 2.0 Consensus size: 82
27981 TATTATAGCC
* * * ** * *
27991 CCCTTAAAATGGTAAAATTTTAATTTAGGCCCTTTCTAATTTATAAA-ATTTTAAACTAGT-AAT
1 CCCTCAAAATGATAAAATTTTAATTTA-ACCCTTTAAAAATTATAAATA-TATAAACTAGTAAAT
28054 AATAAAATTACATTTTTAT
64 AATAAAATTACATTTTTAT
* * *
28073 CCCTCAAAATGATAAATTTTTGATTTAACCCTTTAAAAATTATAAATATATAAACTATTAAAATA
1 CCCTCAAAATGATAAAATTTTAATTTAACCCTTTAAAAATTATAAATATATAAACTAGT-AAATA
*
28138 ATAAAATTATATTTTTA
65 ATAAAATTACATTTTTA
28155 CTATCTTAAA
Statistics
Matches: 68, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
81 24 0.35
82 24 0.35
83 20 0.29
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.41
Consensus pattern (82 bp):
CCCTCAAAATGATAAAATTTTAATTTAACCCTTTAAAAATTATAAATATATAAACTAGTAAATAA
TAAAATTACATTTTTAT
Found at i:31083 original size:2 final size:2
Alignment explanation
Indices: 31076--31104 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31066 TTATTGCATC
31076 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31105 GAATAATGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34796 original size:24 final size:26
Alignment explanation
Indices: 34769--34816 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
34759 AGAGAAATGT
34769 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
34793 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
34817 CCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:34949 original size:27 final size:25
Alignment explanation
Indices: 34900--34970 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 25
34890 GCGCTGTGCA
*
34900 TGCTTCTGTTATCCAGCACTGTGTG
1 TGCTTCTGTTACCCAGCACTGTGTG
*
34925 TGCTTTTGTTACCCAGCACTGTGTG
1 TGCTTCTGTTACCCAGCACTGTGTG
*
34950 TGCTTCTGTTTCCCCAGCACT
1 TGCTTCTG-TTACCCAGCACT
34971 TATGTACCTC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
25 30 0.73
26 11 0.27
ACGTcount: A:0.11, C:0.28, G:0.21, T:0.39
Consensus pattern (25 bp):
TGCTTCTGTTACCCAGCACTGTGTG
Found at i:34982 original size:25 final size:26
Alignment explanation
Indices: 34936--34984 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
34926 GCTTTTGTTA
* * *
34936 CCCAGCACTGTGTGTGCTTCTGTTTC
1 CCCAGCACTGTATGTACCTCTGTTTC
34962 CCCAGCACT-TATGTACCTCTGTT
1 CCCAGCACTGTATGTACCTCTGTT
34985 AAGTACTTCG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 11 0.55
26 9 0.45
ACGTcount: A:0.12, C:0.33, G:0.18, T:0.37
Consensus pattern (26 bp):
CCCAGCACTGTATGTACCTCTGTTTC
Found at i:37565 original size:22 final size:25
Alignment explanation
Indices: 37538--37592 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 25
37528 TTTTGAAATC
37538 TTTTTTAA-TTAAT-TATG-TTTAT
1 TTTTTTAATTTAATGTATGATTTAT
*
37560 TTTTTTAATTTCATGTATGATTTAT
1 TTTTTTAATTTAATGTATGATTTAT
37585 TTATTTTA
1 TT-TTTTA
37593 TTATTTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 8 0.29
23 4 0.14
24 4 0.14
25 7 0.25
26 5 0.18
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.67
Consensus pattern (25 bp):
TTTTTTAATTTAATGTATGATTTAT
Found at i:37791 original size:35 final size:35
Alignment explanation
Indices: 37723--37791 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
37713 AATATAATAT
** *
37723 ATTTTGTTTAACTAAACTTGCAAGTAATTTCTTAG
1 ATTTTGTTTAACTAAACTTGCAAACAATCTCTTAG
*
37758 ATTTTGTTTAACTTAACTTGCAAACAATCTCTTA
1 ATTTTGTTTAACTAAACTTGCAAACAATCTCTTA
37792 AATTGGGTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (35 bp):
ATTTTGTTTAACTAAACTTGCAAACAATCTCTTAG
Found at i:41681 original size:24 final size:24
Alignment explanation
Indices: 41652--41702 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
41642 CTTATTGATA
41652 AGGTTCAACAAAAATTATCAGGAT
1 AGGTTCAACAAAAATTATCAGGAT
*
41676 AGGTTCGACAAAAATTATCAGGAT
1 AGGTTCAACAAAAATTATCAGGAT
41700 AGG
1 AGG
41703 ATACGAGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.24
Consensus pattern (24 bp):
AGGTTCAACAAAAATTATCAGGAT
Found at i:48171 original size:112 final size:112
Alignment explanation
Indices: 47974--48235 Score: 508
Period size: 112 Copynumber: 2.3 Consensus size: 112
47964 TACTTAATTC
*
47974 GATACAAATACAAAAAGAAAAGGGGCCTTGGGATCCCTTGCCTCGTTTAATGAAGAGGTGTAGCG
1 GATACAAACACAAAAAGAAAAGGGGCCTTGGGATCCCTTGCCTCGTTTAATGAAGAGGTGTAGCG
48039 TGGCAAAGTTGAGAACCACATCATCCAATATATTCCGGAAAAACATA
66 TGGCAAAGTTGAGAACCACATCATCCAATATATTCCGGAAAAACATA
48086 GATACAAACACAAAAAGAAAAGGGGCCTTGGGATCCCTTGCCTCGTTTAATGAAGAGGTGTAGCG
1 GATACAAACACAAAAAGAAAAGGGGCCTTGGGATCCCTTGCCTCGTTTAATGAAGAGGTGTAGCG
48151 TGGCAAAGTTGAGAACCACATCATCCAATATATTCCGGAAAAACATA
66 TGGCAAAGTTGAGAACCACATCATCCAATATATTCCGGAAAAACATA
48198 GA-ACAAACACAAAAAGAAAAGGGGCCTTGGGATCCCTT
1 GATACAAACACAAAAAGAAAAGGGGCCTTGGGATCCCTT
48236 CCCTTGCCTC
Statistics
Matches: 149, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
111 36 0.24
112 113 0.76
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.20
Consensus pattern (112 bp):
GATACAAACACAAAAAGAAAAGGGGCCTTGGGATCCCTTGCCTCGTTTAATGAAGAGGTGTAGCG
TGGCAAAGTTGAGAACCACATCATCCAATATATTCCGGAAAAACATA
Found at i:52804 original size:14 final size:14
Alignment explanation
Indices: 52785--52838 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
52775 ATTTCATAAT
52785 AAAAAATATTTTTA
1 AAAAAATATTTTTA
*
52799 AAAAAATTAATTTTA
1 AAAAAA-TATTTTTA
*
52814 ATTAAAATA-TTTTA
1 A-AAAAATATTTTTA
52828 AAATAAATATT
1 AAA-AAATATT
52839 ATTTTAAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 1 0.03
14 17 0.52
15 11 0.33
16 4 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAAAAATATTTTTA
Found at i:52812 original size:15 final size:14
Alignment explanation
Indices: 52785--52846 Score: 54
Period size: 14 Copynumber: 4.1 Consensus size: 14
52775 ATTTCATAAT
*
52785 AAAAAATATTTTTA
1 AAAAAATAATTTTA
52799 AAAAAATTAATTTTA
1 AAAAAA-TAATTTTA
*
52814 ATTAAAAT-ATTTTA
1 A-AAAAATAATTTTA
52828 AAATAAATATTATTTTA
1 AAA-AAATA--ATTTTA
52845 AA
1 AA
52847 CAATCAATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
13 1 0.03
14 17 0.44
15 9 0.23
16 4 0.10
17 8 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAAAAATAATTTTA
Found at i:52822 original size:30 final size:31
Alignment explanation
Indices: 52787--52845 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
52777 TTCATAATAA
52787 AAAATATTTTTAAAA-AAAT-TAATTTTAATT
1 AAAATA-TTTTAAAATAAATATAATTTTAATT
*
52817 AAAATATTTTAAAATAAATATTATTTTAA
1 AAAATATTTTAAAATAAATATAATTTTAA
52846 ACAATCAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 8 0.31
30 10 0.38
31 8 0.31
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
AAAATATTTTAAAATAAATATAATTTTAATT
Found at i:56181 original size:87 final size:87
Alignment explanation
Indices: 56068--56241 Score: 330
Period size: 87 Copynumber: 2.0 Consensus size: 87
56058 GAAACTCCAA
* *
56068 ACCATGCCCTTTCTCTTTGGTCAAATTATTAGGCAAGCTTTGTGGAGCAACGAACTTCACCATAT
1 ACCATGCCCTTTCTCTTTGATCAAATTATTAGGCAAGCTTTGTGGAGCAACGAACTTCACAATAT
56133 TAAAGGTTGGAGAATTTGACAT
66 TAAAGGTTGGAGAATTTGACAT
56155 ACCATGCCCTTTCTCTTTGATCAAATTATTAGGCAAGCTTTGTGGAGCAACGAACTTCACAATAT
1 ACCATGCCCTTTCTCTTTGATCAAATTATTAGGCAAGCTTTGTGGAGCAACGAACTTCACAATAT
56220 TAAAGGTTGGAGAATTTGACAT
66 TAAAGGTTGGAGAATTTGACAT
56242 TTGAGAAGTA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 85 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (87 bp):
ACCATGCCCTTTCTCTTTGATCAAATTATTAGGCAAGCTTTGTGGAGCAACGAACTTCACAATAT
TAAAGGTTGGAGAATTTGACAT
Found at i:56710 original size:32 final size:30
Alignment explanation
Indices: 56674--56786 Score: 113
Period size: 32 Copynumber: 3.6 Consensus size: 30
56664 ACAACCATGA
56674 AAATCCCAAAAATCCCTAAATTTTTAAAACCT
1 AAATCCC-AAAATCCCTAAATTTTT-AAACCT
* *
56706 AAATCCTCAAAATCCCAAAAATTTTAAACTCT
1 AAATCC-CAAAATCCCTAAATTTTTAAAC-CT
* * *
56738 AAAACCCAAAATACCCCACATTTTTTAAACCT
1 AAATCCCAAAAT-CCCTA-AATTTTTAAACCT
56770 AAA--CCAAAATCCCTAAA
1 AAATCCCAAAATCCCTAAA
56787 CCCAATAACC
Statistics
Matches: 69, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
28 1 0.01
29 4 0.06
30 7 0.10
31 10 0.14
32 37 0.54
33 10 0.14
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.25
Consensus pattern (30 bp):
AAATCCCAAAATCCCTAAATTTTTAAACCT
Found at i:56774 original size:31 final size:29
Alignment explanation
Indices: 56682--56782 Score: 96
Period size: 31 Copynumber: 3.3 Consensus size: 29
56672 GAAAATCCCA
*
56682 AAAATCCCTAAATTTTTAAAACCTAAATCCTC
1 AAAATCCC-AAATTTTTTAAACCTAAA-CC-C
**
56714 AAAATCCCAAAAATTTTAAACTCTAAAACCC
1 AAAATCCCAAATTTTTTAAAC-CT-AAACCC
*
56745 AAAATACCCCACATTTTTTAAACCTAAA-CC
1 AAAAT--CCCAAATTTTTTAAACCTAAACCC
56775 AAAATCCC
1 AAAATCCC
56783 TAAACCCAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
28 3 0.05
30 7 0.12
31 19 0.32
32 14 0.24
33 16 0.27
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.26
Consensus pattern (29 bp):
AAAATCCCAAATTTTTTAAACCTAAACCC
Found at i:57023 original size:19 final size:20
Alignment explanation
Indices: 57001--57046 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
56991 GGGTAAATAT
57001 TTTATTGTTTTTAA-TTTAA
1 TTTATTGTTTTTAATTTTAA
57020 TTTA-TG-TTTTAATTTTAA
1 TTTATTGTTTTTAATTTTAA
*
57038 TTTTTTGTT
1 TTTATTGTT
57047 GACATGATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 6 0.26
18 10 0.43
19 6 0.26
20 1 0.04
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.72
Consensus pattern (20 bp):
TTTATTGTTTTTAATTTTAA
Found at i:60943 original size:13 final size:13
Alignment explanation
Indices: 60925--60950 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
60915 AAGGTTAGGC
60925 TTTTTTTTTTTAT
1 TTTTTTTTTTTAT
60938 TTTTTTTTTTTAT
1 TTTTTTTTTTTAT
60951 GATTTACAGT
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:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (13 bp):
TTTTTTTTTTTAT
Found at i:62260 original size:233 final size:231
Alignment explanation
Indices: 61617--62297 Score: 725
Period size: 237 Copynumber: 2.9 Consensus size: 231
61607 TGTCATCCAA
* * *
61617 GGAAAGAATGGTATTATATTGACGGAAAGATTCGCATAGTGATATAGAACCATTATTTTTCTCCT
1 GGAAAGAAT-GTA-TATATTGACCGAAAGGTTCGCATCGTGATATAGAACCATTA-TTTTCTCCT
*
61682 CTGTAGGTGTTAAGGTTGTATGGTTATATTCAATAATT-ACCTGTCTATGAGTGCACTTCGAGTT
63 CTGTAGGTGTTAAGGTTGTATGGTTATATTCAATAATTGA-CTGTCTCTGAGTGCACTTCGAGTT
* * * * *
61746 TTCAATTCTAAGATGGGCGAAGGAGAATTCATGGCTTTTTATGTTCATTATAAGTATAGGAGGGG
127 TTCAATTCTAAGATGAGCGAAGGAGAATTCGTGGCTTTTTATGTTCGTTATAAGTATAAGAAGGG
*
61811 GACAAGTCTGGGAGTTAATGTATTGTTTCGTTATCAACTTGTCATATTT
192 GACAAGTCTGGGAG----T-TA----TTCGTTATCAACTTGTCATATGT
* * * * * * * * *
61860 GG--A-AA-G--TATGTTGACCAAAAGGTTCTCATCATGTTATAGAGCCTTTCCTTTTTTCCCCT
1 GGAAAGAATGTATATATTGACCGAAAGGTTCGCATCGTGATATAGAACC-AT--TATTTTCTCCT
* *
61919 CTGTAGGTGTAAAGGTTGTATGGTTATATTCAATAATTGCCTGTCTCTGAGTGCACTTCGAGTTT
63 CTGTAGGTGTTAAGGTTGTATGGTTATATTCAATAATTGACTGTCTCTGAGTGCACTTCGAGTTT
* * * ** *
61984 TCCATTTTAAGAT-AGGCGAAGGAGAATTTGTTACTTTTTATGTTCGTTATAAGTATAAGAAGGA
128 TCAATTCTAAGATGA-GCGAAGGAGAATTCGTGGCTTTTTATGTTCGTTATAAGTATAAGAAGGG
* * *
62048 GACCAGTGTGGGAGTTA-TCGTTGTCAACTTGTCATATGT
192 GACAAGTCTGGGAGTTATTCGTTATCAACTTGTCATATGT
* *
62087 GGAAAGAATCGTATATATTGGCTGAAAGGTTCGCATCGTGATATAGAACCATTATTCTTCTCCTT
1 GGAAAGAAT-GTATATATTGACCGAAAGGTTCGCATCGTGATATAGAACCATTATT-TTCTCC-T
* * *
62152 TTGTAGGTGTTAAGGTTGTATGGTTATATTCGATAATTGACTGTCTCTGAGTGCACTTTGAGTTT
63 CTGTAGGTGTTAAGGTTGTATGGTTATATTCAATAATTGACTGTCTCTGAGTGCACTTCGAGTTT
* * * **
62217 GT-AATTCTAAGATGAGCAAAGCAGAATTCGTGGCTTGTTATGTTCGTTGCAAGTATAAGAAGGG
128 -TCAATTCTAAGATGAGCGAAGGAGAATTCGTGGCTTTTTATGTTCGTTATAAGTATAAGAAGGG
**
62281 GATGAGTCTGGGAGTTA
192 GACAAGTCTGGGAGTTA
62298 ATATATTGTT
Statistics
Matches: 362, Mismatches: 60, Indels: 42
0.78 0.13 0.09
Matches are distributed among these distances:
227 22 0.06
229 1 0.00
230 2 0.01
231 3 0.01
232 8 0.02
233 126 0.35
234 31 0.09
235 28 0.08
236 1 0.00
237 133 0.37
238 2 0.01
240 2 0.01
241 1 0.00
243 2 0.01
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.37
Consensus pattern (231 bp):
GGAAAGAATGTATATATTGACCGAAAGGTTCGCATCGTGATATAGAACCATTATTTTCTCCTCTG
TAGGTGTTAAGGTTGTATGGTTATATTCAATAATTGACTGTCTCTGAGTGCACTTCGAGTTTTCA
ATTCTAAGATGAGCGAAGGAGAATTCGTGGCTTTTTATGTTCGTTATAAGTATAAGAAGGGGACA
AGTCTGGGAGTTATTCGTTATCAACTTGTCATATGT
Found at i:67323 original size:22 final size:21
Alignment explanation
Indices: 67279--67323 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
67269 ATTGTAATCG
67279 ATAAATTAAATGTAAAATTAA
1 ATAAATTAAATGTAAAATTAA
*
67300 ATAAATTTACAAT-TAATATTAA
1 ATAAA-TTA-AATGTAAAATTAA
67322 AT
1 AT
67324 TTATTTCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 5 0.24
22 13 0.62
23 3 0.14
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
ATAAATTAAATGTAAAATTAA
Found at i:70355 original size:13 final size:13
Alignment explanation
Indices: 70337--70362 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
70327 TTTGTTGTGT
70337 TGGGAAAGTTAGG
1 TGGGAAAGTTAGG
70350 TGGGAAAGTTAGG
1 TGGGAAAGTTAGG
70363 CCACAAATAA
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:0.00, G:0.46, T:0.23
Consensus pattern (13 bp):
TGGGAAAGTTAGG
Found at i:71569 original size:28 final size:28
Alignment explanation
Indices: 71509--71572 Score: 94
Period size: 27 Copynumber: 2.3 Consensus size: 28
71499 TGGGGTGTAG
71509 GGATTAAATTAAAATATAATTTTTTAAA
1 GGATTAAATTAAAATATAATTTTTTAAA
* * *
71537 -AATTAAATTAAAATTTTATTTTTTAAA
1 GGATTAAATTAAAATATAATTTTTTAAA
71564 GGATTAAAT
1 GGATTAAAT
71573 GTAATTTGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 24 0.77
28 7 0.23
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (28 bp):
GGATTAAATTAAAATATAATTTTTTAAA
Found at i:79301 original size:39 final size:39
Alignment explanation
Indices: 79202--79310 Score: 173
Period size: 39 Copynumber: 2.8 Consensus size: 39
79192 AGGTCCTCAC
* * * * *
79202 GTTCAAGATGGGTAGTTCAATCCAAAAGATGTATATTGA
1 GTTCAACATGGGTAGTACAATTCGAAATATGTATATTGA
79241 GTTCAACATGGGTAGTACAATTCGAAATATGTATATTGA
1 GTTCAACATGGGTAGTACAATTCGAAATATGTATATTGA
79280 GTTCAACATGGGTAGTACAATTCGAAATATG
1 GTTCAACATGGGTAGTACAATTCGAAATATG
79311 CTTCGAATGT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 65 1.00
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (39 bp):
GTTCAACATGGGTAGTACAATTCGAAATATGTATATTGA
Found at i:92590 original size:10 final size:10
Alignment explanation
Indices: 92571--92601 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
92561 TTAAAAAACT
92571 TATATATGTA
1 TATATATGTA
*
92581 TATATGTGTA
1 TATATATGTA
92591 TATATATGTA
1 TATATATGTA
92601 T
1 T
92602 GAACACACGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (10 bp):
TATATATGTA
Found at i:93533 original size:264 final size:268
Alignment explanation
Indices: 93048--93598 Score: 697
Period size: 264 Copynumber: 2.1 Consensus size: 268
93038 TTTCGGTGGC
*
93048 ATTTTGTCTTTAGGGTTTTAAAATATATATAATGATATCTTAGGGAAAAAAAGTTGTTTTTTTAT
1 ATTTTGTCTTTAGGGTTTTAAAATATATAAAATGATATCTTA-GGAAAAAAAGTTG--TTTTTAT
* * * * *
93113 GTATTCGATAATTAAGTTAGATCCCGATTAAATTTAAAGTCGAATTTTTAAATGAAAGTAAAATT
63 GTATTCGATAATCAAGTTAAATCCCGATTAAATCTAAAGTCGAACTTTTAAATGAAAGCAAAATT
** * * * * *
93178 CTTCCTGATTTTTTTTTATTTTTCTTCTATCTTATTCGAAATTGAAACCTTAAAAATGAGGAGTA
128 CTT-CT-ATACTCTTTTATTTTTCTTCCAACATATTCGAAATTGAAACCTTAAAAAGGAGGAGTA
* * *
93243 TAATCGAAATGAGTCAAACTCGAATAATAGT-GATCTCGAATTTGACTCAAAATTTAAGTCTCGA
191 TAATCGAAACGAGTCAAACTCGAATAATAGTAG-TCTCGAACTTGACTCAAAATTTAAGTCTCAA
93307 AATCCTTTAATGGT
255 AATCCTTTAATGGT
* * *
93321 ATTTTATCTTTAGGGTTTTAAAATATATAAAATGATCTCTTA-GAAAAATAGTTG-TTTTATGTA
1 ATTTTGTCTTTAGGGTTTTAAAATATATAAAATGATATCTTAGGAAAAAAAGTTGTTTTTATGTA
* * * *
93384 TT-GAATAATCACA-TTAAATCCCGATTAAATCTAGAGTCGAACTTTTAAATGGAGGCAAAGTTC
66 TTCG-ATAATCA-AGTTAAATCCCGATTAAATCTAAAGTCGAACTTTTAAATGAAAGCAAAATTC
93447 TT-T-TACTCTTTTATTTTTCTTCCAACATATTC-AAATTTGAAACCTTAAAAAGGAGGAGTATA
129 TTCTATACTCTTTTATTTTTCTTCCAACATATTCGAAA-TTGAAACCTTAAAAAGGAGGAGTATA
* * *
93509 ATTGAAACG-GGCTAAACTCGAATAATAGTAGTCTCGAACTTGACTCAAAATTTAAGTTTCAAAA
193 ATCGAAACGAGTC-AAACTCGAATAATAGTAGTCTCGAACTTGACTCAAAATTTAAGTCTCAAAA
*
93573 TCTTTTAATGGT
257 TCCTTTAATGGT
*
93585 ATTTTGTTTTTAGG
1 ATTTTGTCTTTAGG
93599 ATTTAAACTC
Statistics
Matches: 244, Mismatches: 29, Indels: 19
0.84 0.10 0.07
Matches are distributed among these distances:
263 5 0.02
264 124 0.51
265 1 0.00
266 1 0.00
267 1 0.00
268 61 0.25
269 1 0.00
271 11 0.05
273 39 0.16
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (268 bp):
ATTTTGTCTTTAGGGTTTTAAAATATATAAAATGATATCTTAGGAAAAAAAGTTGTTTTTATGTA
TTCGATAATCAAGTTAAATCCCGATTAAATCTAAAGTCGAACTTTTAAATGAAAGCAAAATTCTT
CTATACTCTTTTATTTTTCTTCCAACATATTCGAAATTGAAACCTTAAAAAGGAGGAGTATAATC
GAAACGAGTCAAACTCGAATAATAGTAGTCTCGAACTTGACTCAAAATTTAAGTCTCAAAATCCT
TTAATGGT
Found at i:94400 original size:16 final size:16
Alignment explanation
Indices: 94379--94412 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
94369 ATAAGTACAT
94379 ATTATTTAAAAAAAAA
1 ATTATTTAAAAAAAAA
**
94395 ATTATTTCCAAAAAAA
1 ATTATTTAAAAAAAAA
94411 AT
1 AT
94413 AAAAAAAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTATTTAAAAAAAAA
Found at i:98441 original size:28 final size:29
Alignment explanation
Indices: 98409--98464 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
98399 ATTCTTAGAC
*
98409 AAAAATT-AAAATTTAGCCC-ATGTACTTA
1 AAAAATTAAAAATTAAGCCCTAT-TACTTA
98437 AAAAATTAAAAATTAAGCCCTATTACTT
1 AAAAATTAAAAATTAAGCCCTATTACTT
98465 TTCTAATTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 7 0.28
29 16 0.64
30 2 0.08
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.32
Consensus pattern (29 bp):
AAAAATTAAAAATTAAGCCCTATTACTTA
Found at i:100979 original size:18 final size:19
Alignment explanation
Indices: 100941--100979 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
100931 TTAAAATACA
* *
100941 TAAAAAAAACTTCAATTTT
1 TAAAAAAAACTTAAATCTT
100960 TAAAAAAAA-TTAAATCTT
1 TAAAAAAAACTTAAATCTT
100978 TA
1 TA
100980 TTTTTTTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAAAAAAACTTAAATCTT
Found at i:109302 original size:29 final size:31
Alignment explanation
Indices: 109258--109316 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 31
109248 AAAATAGAAA
*
109258 GACTAAATTCCTAGATAT-AAAT-GTACAAG
1 GACTAAATTCCAAGATATCAAATAGTACAAG
* *
109287 GACTAAATTTCAAGATTTCAAATAGTACAA
1 GACTAAATTCCAAGATATCAAATAGTACAA
109317 TAACTTATGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 15 0.60
30 4 0.16
31 6 0.24
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.29
Consensus pattern (31 bp):
GACTAAATTCCAAGATATCAAATAGTACAAG
Found at i:124195 original size:11 final size:10
Alignment explanation
Indices: 124147--124203 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 10
124137 TGTTCTGAGC
*
124147 ATTTTATTTT
1 ATTTTCTTTT
124157 -TTTTCTTTT
1 ATTTTCTTTT
*
124166 ATATTCTTTT
1 ATTTTCTTTT
124176 AACTTTTCTTCTT
1 -A-TTTTCTT-TT
124189 ATTTTC-TTT
1 ATTTTCTTTT
124198 ATTTTC
1 ATTTTC
124204 CATTCTCTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
9 16 0.40
10 9 0.22
11 6 0.15
12 7 0.17
13 2 0.05
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTTCTTTT
Found at i:129194 original size:109 final size:111
Alignment explanation
Indices: 128909--129196 Score: 318
Period size: 113 Copynumber: 2.6 Consensus size: 111
128899 ACGTTATTCG
* * * * * **
128909 GATTCGAGTATGAGCGTTAAAAT-GGTTTTTTAACAAATTGCCTTTTAGG-TTTTGTGACAATGA
1 GATTCAAGTGTGAGCGTT-AAATCGGTTTTTTAACGAATTGCCTTTTTGGAGTTTGTTTCAATGA
** * * *
128972 TAGGTTTTAATTGATAGTTTGTTTAGAGGATTCTTTAACTACGCTATTTA
65 TACATTCTAATTGATAATTTATTTAGAGGATTCTTTAACT---CTATTTA
* * *
129022 GATTCGAGTGTGAGCGTTAAATTGGTTTTTTAATGAATTGCCTTTTTGGAGTTTGTTTCAATGAT
1 GATTCAAGTGTGAGCGTTAAATCGGTTTTTTAACGAATTGCCTTTTTGGAGTTTGTTTCAATGAT
* *
129087 ACATTCTGATTGATAATTTATTTAGAGGATTCTTT-A-T-TATTTG
66 ACATTCTAATTGATAATTTATTTAGAGGATTCTTTAACTCTATTTA
*
129130 GATTCAAGTGTGAGTGTTAAATACCGG-TTTTTAACGAATTGCCTTTTTGGAGTTTGTTTCAATG
1 GATTCAAGTGTGAGCGTTAAAT--CGGTTTTTTAACGAATTGCCTTTTTGGAGTTTGTTTCAATG
129194 ATA
64 ATA
129197 GTTTTTGATT
Statistics
Matches: 153, Mismatches: 18, Indels: 12
0.84 0.10 0.07
Matches are distributed among these distances:
108 25 0.16
109 39 0.25
110 2 0.01
112 5 0.03
113 41 0.27
114 41 0.27
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.45
Consensus pattern (111 bp):
GATTCAAGTGTGAGCGTTAAATCGGTTTTTTAACGAATTGCCTTTTTGGAGTTTGTTTCAATGAT
ACATTCTAATTGATAATTTATTTAGAGGATTCTTTAACTCTATTTA
Found at i:129206 original size:109 final size:111
Alignment explanation
Indices: 128909--129209 Score: 335
Period size: 109 Copynumber: 2.7 Consensus size: 111
128899 ACGTTATTCG
* * * * * **
128909 GATTCGAGTATGAGCGTTAAAAT-GGTTTTTTAACAAATTGCCTTTTAGG-TTTTGTGACAATGA
1 GATTCAAGTGTGAGCGTT-AAATCGGTTTTTTAACGAATTGCCTTTTTGGAGTTTGTTTCAATGA
* * * *
128972 TAGGTTTTAATTGATAGTTTGTTTAGAGGATTCTTTAACTACGCTATTTA
65 TAGATTTTGATTGATAATTTATTTAGAGGATTCTTTAACT---CTATTTA
* * *
129022 GATTCGAGTGTGAGCGTTAAATTGGTTTTTTAATGAATTGCCTTTTTGGAGTTTGTTTCAATGAT
1 GATTCAAGTGTGAGCGTTAAATCGGTTTTTTAACGAATTGCCTTTTTGGAGTTTGTTTCAATGAT
* * *
129087 ACATTCTGATTGATAATTTATTTAGAGGATTCTTT-A-T-TATTTG
66 AGATTTTGATTGATAATTTATTTAGAGGATTCTTTAACTCTATTTA
*
129130 GATTCAAGTGTGAGTGTTAAATACCGG-TTTTTAACGAATTGCCTTTTTGGAGTTTGTTTCAATG
1 GATTCAAGTGTGAGCGTTAAAT--CGGTTTTTTAACGAATTGCCTTTTTGGAGTTTGTTTCAATG
*
129194 ATAGTTTTTGATTGAT
64 ATAGATTTTGATTGAT
129210 TGTTTCTTTA
Statistics
Matches: 163, Mismatches: 21, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
108 25 0.15
109 49 0.30
110 2 0.01
112 5 0.03
113 41 0.25
114 41 0.25
ACGTcount: A:0.25, C:0.08, G:0.21, T:0.46
Consensus pattern (111 bp):
GATTCAAGTGTGAGCGTTAAATCGGTTTTTTAACGAATTGCCTTTTTGGAGTTTGTTTCAATGAT
AGATTTTGATTGATAATTTATTTAGAGGATTCTTTAACTCTATTTA
Found at i:131446 original size:2 final size:2
Alignment explanation
Indices: 131439--131476 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
131429 AAGGAGATAG
* *
131439 TC TC TC TC TC TC TC TC TC TC TC TC AC TC TC AC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
131477 GTGTTTCGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.05, C:0.50, G:0.00, T:0.45
Consensus pattern (2 bp):
TC
Found at i:137188 original size:7 final size:7
Alignment explanation
Indices: 137176--137204 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
137166 TTATGTACGA
137176 AGTGAAT
1 AGTGAAT
137183 AGTGAAT
1 AGTGAAT
137190 AGTGAAT
1 AGTGAAT
137197 AGTGAAT
1 AGTGAAT
137204 A
1 A
137205 ATTGAAAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.28, T:0.28
Consensus pattern (7 bp):
AGTGAAT
Done.