Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1615
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: 41816
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:957 original size:21 final size:21
Alignment explanation
Indices: 924--968 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
914 TTGCAAGTTG
*
924 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
946 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
966 AAA
1 AAA
969 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:2790 original size:15 final size:15
Alignment explanation
Indices: 2770--2800 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2760 TAAAAATGTC
*
2770 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
2785 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
2800 C
1 C
2801 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:4900 original size:13 final size:13
Alignment explanation
Indices: 4882--4906 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4872 CATTTTTCTT
4882 TGTATCGATACAA
1 TGTATCGATACAA
4895 TGTATCGATACA
1 TGTATCGATACA
4907 GGGTGATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:11093 original size:4 final size:4
Alignment explanation
Indices: 11084--11110 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
11074 ACAAAAAAAC
11084 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
11111 CACCTCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:13406 original size:130 final size:130
Alignment explanation
Indices: 13256--13669 Score: 480
Period size: 130 Copynumber: 3.2 Consensus size: 130
13246 GTATCCCTCA
* * * ** * *
13256 AAAATAACGAGGTTGCAGTATCCACGATTGTG-GAAAATCGATGCTATAGAAATAAGGCTGGGGT
1 AAAATAA-GAGGTTGGAGTATCCCCGATTGTGAG-AAATCAATATTTTAGAAATAAAGCTGGGGT
* *
13320 TGGAGTATCCCCGTGAAAATAATGGGATTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTAGA
64 TGGAGTATCCCC-TGAAAATAACGGGATTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTAGA
13385 AAT
128 AAT
*
13388 AAAATAAG-GGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGTTGGGGTTG
1 AAAATAAGAGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCTGGGGTTG
* ** * *
13452 GAGTATCCCCTCGGAAATAACAAGATTAGAGCATCCCCGATTATGAAAAGATTGGTGTTTTAGAA
66 GAGTATCCCCT-GAAAATAACGGGATTGGAGTATCCCCGATTATGAAAA-ATTGGTGTTTTAGAA
13517 AT
129 AT
* * * *
13519 AAAAT-TGCA-GTTAGAGTATCCCCAATTGTGAGAAATCAATATTTTAGAAATAAAGCCGGGGTT
1 AAAATAAG-AGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCTGGGGTT
* * * *
13582 AGAGTATCCCCTTAGAAATAAGGGGATTGGAGTATCCCCGATTATGAAAAATTGATGTTTT-GAA
65 GGAGTATCCCCTGA-AAATAACGGGATTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTAG-A
13646 AAT
128 AAT
** *
13649 AAAA-CCGAGGTTAGAGTATCC
1 AAAATAAGAGGTTGGAGTATCC
13670 TCGAGATGAA
Statistics
Matches: 243, Mismatches: 30, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
129 3 0.01
130 118 0.49
131 115 0.47
132 7 0.03
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.28
Consensus pattern (130 bp):
AAAATAAGAGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAATAAAGCTGGGGTTG
GAGTATCCCCTGAAAATAACGGGATTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTAGAAAT
Found at i:13409 original size:51 final size:51
Alignment explanation
Indices: 13335--13461 Score: 164
Period size: 51 Copynumber: 2.5 Consensus size: 51
13325 TATCCCCGTG
*** *
13335 AAAATAATGGGATTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTAGAAAT
1 AAAATAA-GGG-TTGGAGTATCCCCGATTGTGAAAAATCAATATTTTAGAAAT
*
13388 AAAATAAGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTAGAAAT
1 AAAATAAGGGTTGGAGTATCCCCGATTGTGAAAAATCAATATTTTAGAAAT
* **
13439 AAAGTTGGGGTTGGAGTATCCCC
1 AAAATAAGGGTTGGAGTATCCCC
13462 TCGGAAATAA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
51 56 0.85
52 3 0.05
53 7 0.11
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (51 bp):
AAAATAAGGGTTGGAGTATCCCCGATTGTGAAAAATCAATATTTTAGAAAT
Found at i:13559 original size:131 final size:128
Alignment explanation
Indices: 13302--13669 Score: 477
Period size: 131 Copynumber: 2.8 Consensus size: 128
13292 ATCGATGCTA
* * * *
13302 TAGAAATAAGGCTGGGGTTGGAGTATCCCCGTGAAAATAATGGGATTGGAGTATCCCCGATTGTG
1 TAGAAATAAAGCTGGGGTTGGAGTATCCCC-TGGAAATAACGGGATTGGAGTATCCCCGATTATG
* * *
13367 AAAAATTGGTGTTTTAGAAATAAAATAAGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTT
65 AAAAATTGGTGTTTTAGAAATAAAAT-AGAGTTAGAGTATCCCCAATTGTGAGAAATCAATATTT
* ** * *
13432 TAGAAATAAAGTTGGGGTTGGAGTATCCCCTCGGAAATAACAAGATTAGAGCATCCCCGATTATG
1 TAGAAATAAAGCTGGGGTTGGAGTATCCCCT-GGAAATAACGGGATTGGAGTATCCCCGATTATG
*
13497 AAAAGATTGGTGTTTTAGAAATAAAATTGCAGTTAGAGTATCCCCAATTGTGAGAAATCAATATT
65 AAAA-ATTGGTGTTTTAGAAATAAAATAG-AGTTAGAGTATCCCCAATTGTGAGAAATCAATATT
13562 T
128 T
* * * *
13563 TAGAAATAAAGCCGGGGTTAGAGTATCCCCTTAGAAATAAGGGGATTGGAGTATCCCCGATTATG
1 TAGAAATAAAGCTGGGGTTGGAGTATCCCC-TGGAAATAACGGGATTGGAGTATCCCCGATTATG
* **
13628 AAAAATTGATGTTTT-GAAAATAAAACCGAGGTTAGAGTATCC
65 AAAAATTGGTGTTTTAG-AAATAAAATAGA-GTTAGAGTATCC
13670 TCGAGATGAA
Statistics
Matches: 207, Mismatches: 25, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
129 3 0.01
130 90 0.43
131 113 0.55
132 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.28
Consensus pattern (128 bp):
TAGAAATAAAGCTGGGGTTGGAGTATCCCCTGGAAATAACGGGATTGGAGTATCCCCGATTATGA
AAAATTGGTGTTTTAGAAATAAAATAGAGTTAGAGTATCCCCAATTGTGAGAAATCAATATTT
Found at i:15992 original size:49 final size:50
Alignment explanation
Indices: 15939--16068 Score: 201
Period size: 49 Copynumber: 2.6 Consensus size: 50
15929 AAAAATGCCT
* * *
15939 GAATGTATCGATACATTGAAAAATGTATCGATACATCTGGGT-AAACCTA
1 GAATGTATCGATACAATGAACAATGTATCGATACATCTGGGTCAAACCCA
15988 GAATGTATCGATACAATGAACAATGTATCGATACATCTGGGTCAAACCCA
1 GAATGTATCGATACAATGAACAATGTATCGATACATCTGGGTCAAACCCA
* *
16038 GAATATATTGATACAAT-AACAATGTATCGAT
1 GAATGTATCGATACAATGAACAATGTATCGAT
16069 GCAAATTATG
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
49 54 0.72
50 21 0.28
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (50 bp):
GAATGTATCGATACAATGAACAATGTATCGATACATCTGGGTCAAACCCA
Found at i:16856 original size:22 final size:22
Alignment explanation
Indices: 16818--16867 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
16808 ATCAAATCTT
16818 CTTC-AAATATCTTATTTTTCA
1 CTTCAAAATATCTTATTTTTCA
16839 CTTCAAAATA-CTTCATTTTTCA
1 CTTCAAAATATCTT-ATTTTTCA
16861 --TCAAAAT
1 CTTCAAAAT
16868 CATCAACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 7 0.26
21 7 0.26
22 13 0.48
ACGTcount: A:0.34, C:0.20, G:0.00, T:0.46
Consensus pattern (22 bp):
CTTCAAAATATCTTATTTTTCA
Found at i:20767 original size:97 final size:97
Alignment explanation
Indices: 20593--21094 Score: 440
Period size: 97 Copynumber: 5.2 Consensus size: 97
20583 CTTTTAAATC
*
20593 TTTT-TCTAAAAGCCCATGACTCAGTGGCATCTCTTTTCCAAGTCCACGACTTAGTGGCATATTT
1 TTTTCTCTCAAAGCCCATGACTCAGTGGCATCTCTTTTCCAAGTCCACGACTTAGTGGCATATTT
*
20657 TTTCTTCCAAGTCCACGATTTAGTGGCATTAT
66 TTTCTTCCAAGTCCACGATTTAGTGGCATCAT
*
20689 TTTTCTCTCAAAGCCCATGACTTAGTGGCATCTCTTTTCCAAGTCCACGACTTAGTGGCATATTT
1 TTTTCTCTCAAAGCCCATGACTCAGTGGCATCTCTTTTCCAAGTCCACGACTTAGTGGCATATTT
*
20754 TTTCTTCCAAGTCCACGGTTTAGTGGCATCAT
66 TTTCTTCCAAGTCCACGATTTAGTGGCATCAT
** *
20786 TTTTCTCTCAAAGCCCATGACTCAGTGGTGTCTCTTTTCCAAGTCCACGACTCT-GTGGC--A-C
1 TTTTCTCTCAAAGCCCATGACTCAGTGGCATCTCTTTTCCAAGTCCACGACT-TAGTGGCATATT
** ** * *
20847 CCTTC--CCAAAGTCCATAACTTAGTAGCATC-T
65 TTTTCTTCC-AAGTCCACGATTTAGTGGCATCAT
* * * ** * *
20878 TTTT-TC-C-AAGTCCACGACTCAGTGGCATTCTTTTTCTTCCAAGTCCATAATTTAGTGGCATC
1 TTTTCTCTCAAAGCCCATGACTCAGTGGCA-TC-TCTT-TTCCAAGTCCACGACTTAGTGGCATA
* * *
20940 CTTTTTCTTCCAAGTCCATGATTCAGTGGCATC--
63 TTTTTTCTTCCAAGTCCACGATTTAGTGGCATCAT
* * * * * * * * * * *
20973 TCTTCTCT--AAGTCCATGACTTAGTGACATCTTTTTTCTTCCAAGCCCATGACTCAATGGTATC
1 TTTTCTCTCAAAGCCCATGACTCAGTGGCATC--TCTT-TTCCAAGTCCACGACTTAGTGGCATA
* * ** * *
21036 CTTTTTCTTCCAAGTCCATGACATAGTGGCAACCT
63 TTTTTTCTTCCAAGTCCACGATTTAGTGGCATCAT
* *
21071 TTTTCTTTTCAAAGCCCATAACTC
1 TTTTC-TCTCAAAGCCCATGACTC
21095 TTTGGTACCC
Statistics
Matches: 336, Mismatches: 50, Indels: 35
0.80 0.12 0.08
Matches are distributed among these distances:
89 16 0.05
90 3 0.01
91 6 0.02
92 25 0.07
93 17 0.05
94 3 0.01
95 9 0.03
96 96 0.29
97 144 0.43
98 5 0.01
99 2 0.01
101 10 0.03
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.37
Consensus pattern (97 bp):
TTTTCTCTCAAAGCCCATGACTCAGTGGCATCTCTTTTCCAAGTCCACGACTTAGTGGCATATTT
TTTCTTCCAAGTCCACGATTTAGTGGCATCAT
Found at i:20985 original size:63 final size:64
Alignment explanation
Indices: 20606--21077 Score: 342
Period size: 63 Copynumber: 7.4 Consensus size: 64
20596 TTCTAAAAGC
* * * * *
20606 CCATGACTCAGTGGCAT-C-TCTT-TTCCAAGTCCACGACTTAGTGGCATATTTTTTCTTCCAAG
1 CCATGACTTAGTGGCATCCTTTTTCTTCCAAGTCCACGACTCAGTGGCAT-CTTCTTC-TCCAAG
20668 T
64 T
* * ** * * * * *
20669 CCACGATTTAGTGGCATTATTTTTCTCTCAAAGCCCATGACTTAGTGGCATC-TCTTTTCCAAGT
1 CCATGACTTAGTGGCATCCTTTTTCT-TCCAAGTCCACGACTCAGTGGCATCTTCTTCTCCAAGT
* ** ** * *
20733 CCACGACTTAGTGGCATATTTTTTCTTCCAAGTCCACGGTTTAGTGGCATCATTTTTCTCTCAAA
1 CCATGACTTAGTGGCATCCTTTTTCTTCCAAGTCCACGACTCAGTGGCATC-TTCTTCTC-C-AA
*
20798 GC
63 GT
* ** * * *
20800 CCATGACTCAGTGGTGT-C-TCTT-TTCCAAGTCCACGACTCTGTGGCA-C-CCTTC-CCAAAGT
1 CCATGACTTAGTGGCATCCTTTTTCTTCCAAGTCCACGACTCAGTGGCATCTTCTTCTCC-AAGT
* * *
20859 CCATAACTTAGTAGCAT-C-TTTT-TTCCAAGTCCACGACTCAGTGGCATTCTTTTTCTTCCAAG
1 CCATGACTTAGTGGCATCCTTTTTCTTCCAAGTCCACGACTCAGTGGCA-TCTTCTTC-TCCAAG
20921 T
64 T
* * * * *
20922 CCATAATTTAGTGGCATCCTTTTTCTTCCAAGTCCATGATTCAGTGGCATC-TCTTCTCTAAGT
1 CCATGACTTAGTGGCATCCTTTTTCTTCCAAGTCCACGACTCAGTGGCATCTTCTTCTCCAAGT
* * * * * * *
20985 CCATGACTTAGTGACATCTTTTTTCTTCCAAGCCCATGACTCAATGGTATCCTTTTTCTTCCAAG
1 CCATGACTTAGTGGCATCCTTTTTCTTCCAAGTCCACGACTCAGTGGCAT-CTTCTTC-TCCAAG
21050 T
64 T
* *
21051 CCATGACATAGTGGCAACCTTTTTCTT
1 CCATGACTTAGTGGCATCCTTTTTCTT
21078 TTCAAAGCCC
Statistics
Matches: 326, Mismatches: 64, Indels: 35
0.77 0.15 0.08
Matches are distributed among these distances:
59 44 0.13
60 1 0.00
61 4 0.01
62 3 0.01
63 102 0.31
64 58 0.18
65 24 0.07
66 53 0.16
67 37 0.11
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.37
Consensus pattern (64 bp):
CCATGACTTAGTGGCATCCTTTTTCTTCCAAGTCCACGACTCAGTGGCATCTTCTTCTCCAAGT
Found at i:21064 original size:96 final size:96
Alignment explanation
Indices: 20855--21066 Score: 257
Period size: 96 Copynumber: 2.2 Consensus size: 96
20845 ACCCTTCCCA
* * * * *
20855 AAGTCCATAACTTAGTAGCATCTTTTTTCCAAGTCCACGACTCAGTGGCATTCTTTTTCTTCCAA
1 AAGTCCATGACTTAGTGGCATCTCTTCTCCAAGTCCACGACTCAGTGACATTCTTTTTCTTCCAA
* * * *
20920 GTCCATAATTTAGTGGCATCCTTTTTCTTCC
66 GCCCATAACTCAATGGCATCCTTTTTCTTCC
* * *
20951 AAGTCCATGA-TTCAGTGGCATCTCTTCTCTAAGTCCATGACTTAGTGACA-TCTTTTTTCTTCC
1 AAGTCCATGACTT-AGTGGCATCTCTTCTCCAAGTCCACGACTCAGTGACATTC-TTTTTCTTCC
* *
21014 AAGCCCATGACTCAATGGTATCCTTTTTCTTCC
64 AAGCCCATAACTCAATGGCATCCTTTTTCTTCC
*
21047 AAGTCCATGACATAGTGGCA
1 AAGTCCATGACTTAGTGGCA
21067 ACCTTTTTCT
Statistics
Matches: 98, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
95 4 0.04
96 93 0.95
97 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (96 bp):
AAGTCCATGACTTAGTGGCATCTCTTCTCCAAGTCCACGACTCAGTGACATTCTTTTTCTTCCAA
GCCCATAACTCAATGGCATCCTTTTTCTTCC
Found at i:21072 original size:33 final size:34
Alignment explanation
Indices: 20606--21077 Score: 303
Period size: 33 Copynumber: 14.8 Consensus size: 34
20596 TTCTAAAAGC
*
20606 CCATGAC-TCAGTGGCAT-C-TCTT-TTCCAAGT
1 CCATGACTTCAGTGGCATCCTTTTTCTTCCAAGT
* **
20636 CCACGACTT-AGTGGCATATTTTTTCTTCCAAGT
1 CCATGACTTCAGTGGCATCCTTTTTCTTCCAAGT
* * ** * *
20669 CCACGA-TTTAGTGGCATTATTTTTCTCTCAAAGC
1 CCATGACTTCAGTGGCATCCTTTTTCT-TCCAAGT
*
20703 CCATGACTT-AGTGGCAT-C-TCTT-TTCCAAGT
1 CCATGACTTCAGTGGCATCCTTTTTCTTCCAAGT
* **
20733 CCACGACTT-AGTGGCATATTTTTTCTTCCAAGT
1 CCATGACTTCAGTGGCATCCTTTTTCTTCCAAGT
* * * * * *
20766 CCACG-GTTTAGTGGCATCATTTTTCTCTCAAAGC
1 CCATGACTTCAGTGGCATCCTTTTTCT-TCCAAGT
** *
20800 CCATGAC-TCAGTGGTGT-C-TCTT-TTCCAAGT
1 CCATGACTTCAGTGGCATCCTTTTTCTTCCAAGT
* * *
20830 CCACGAC-TCTGTGGCA-CC--CTTC--CCAAAGT
1 CCATGACTTCAGTGGCATCCTTTTTCTTCC-AAGT
* *
20859 CCATAACTT-AGTAGCAT-C-TTTT-TTCCAAGT
1 CCATGACTTCAGTGGCATCCTTTTTCTTCCAAGT
* *
20889 CCACGAC-TCAGTGGCATTCTTTTTCTTCCAAGT
1 CCATGACTTCAGTGGCATCCTTTTTCTTCCAAGT
* *
20922 CCAT-AATTTAGTGGCATCCTTTTTCTTCCAAGT
1 CCATGACTTCAGTGGCATCCTTTTTCTTCCAAGT
* *
20955 CCATGA-TTCAGTGGCAT-C-TCTTC-TCTAAGT
1 CCATGACTTCAGTGGCATCCTTTTTCTTCCAAGT
* * *
20985 CCATGACTT-AGTGACATCTTTTTTCTTCCAAGC
1 CCATGACTTCAGTGGCATCCTTTTTCTTCCAAGT
* *
21018 CCATGAC-TCAATGGTATCCTTTTTCTTCCAAGT
1 CCATGACTTCAGTGGCATCCTTTTTCTTCCAAGT
* *
21051 CCATGACAT-AGTGGCAACCTTTTTCTT
1 CCATGACTTCAGTGGCATCCTTTTTCTT
21078 TTCAAAGCCC
Statistics
Matches: 348, Mismatches: 61, Indels: 63
0.74 0.13 0.13
Matches are distributed among these distances:
28 2 0.01
29 19 0.05
30 91 0.26
31 12 0.03
32 27 0.08
33 159 0.46
34 36 0.10
35 2 0.01
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.37
Consensus pattern (34 bp):
CCATGACTTCAGTGGCATCCTTTTTCTTCCAAGT
Found at i:21146 original size:33 final size:33
Alignment explanation
Indices: 21103--21667 Score: 233
Period size: 34 Copynumber: 17.0 Consensus size: 33
21093 TCTTTGGTAC
*
21103 CCTTTTAAGTCTACAACTCCATGGCACCTTTTT
1 CCTTTTAAGTCCACAACTCCATGGCACCTTTTT
* * *
21136 CCCTTGAAGT-CAGCAACTCAATGGCACCCTTTTT
1 CCTTTTAAGTCCA-CAACTCCATGGCA-CCTTTTT
* * *
21170 CCTTTTAAGTCCATAATTCTATGGCACCTTTCTT
1 CCTTTTAAGTCCACAACTCCATGGCACCTTT-TT
* *
21204 CCTTTTAAGTCCACAACTCCATGGCCCCCATAACTCTGTGG
1 CCTTTTAAGTCCACAACTCCATGG-CACC-T---T-T-T-T
*
21245 CACTTTTTTTCCCTTAAGTCCACAACT-CAGTGGCGCCCTTTTT
1 C-C--T---T---TTAAGTCCACAACTCCA-TGGC-ACCTTTTT
* * *
21288 CCTTTTAAGTCCATAACTTCGTGGCACCTTTTT
1 CCTTTTAAGTCCACAACTCCATGGCACCTTTTT
* * * *
21321 CCCTTTAAATCCATAACTCAATGGCACCTTTTTT
1 CCTTTTAAGTCCACAACTCCATGGCACC-TTTTT
* * * **
21355 CCTTTTAAATCCATAATTCTGTGGCACC-TTTT
1 CCTTTTAAGTCCACAACTCCATGGCACCTTTTT
* * *
21387 CCTTTCAAGTCCATAACTCTATGGCACC----T
1 CCTTTTAAGTCCACAACTCCATGGCACCTTTTT
* *
21416 --TTTTAAATCCACAAATCCATGGCACCTTTTT
1 CCTTTTAAGTCCACAACTCCATGGCACCTTTTT
* * * * * * **
21447 -CTTTTCAAAGCCCATAATTTCGTGACACTCTTTCA
1 CCTTTT--AAGTCCACAACTCCATGGCAC-CTTTTT
* *
21482 CCTTTTAAGTCCACAACTCTATGGCACCCATTTT
1 CCTTTTAAGTCCACAACTCCATGGCA-CCTTTTT
* **
21516 GCTTTTAAGTCCACAACTCTGTGGCA-C-----
1 CCTTTTAAGTCCACAACTCCATGGCACCTTTTT
* * * *
21543 CCTTTTATGTCTACAACTCCGTGGCA-CATTTT
1 CCTTTTAAGTCCACAACTCCATGGCACCTTTTT
* *
21575 CCTTCTAAGTCCACATCTCCATGGCA-C-----
1 CCTTTTAAGTCCACAACTCCATGGCACCTTTTT
* * *
21602 CCTTTTAAGTCCACAACTCTATGCCACCATTTT
1 CCTTTTAAGTCCACAACTCCATGGCACCTTTTT
* * **
21635 CCCTTTAACAT-CACAACTCTGTGGCACCTTTTT
1 CCTTTTAA-GTCCACAACTCCATGGCACCTTTTT
21668 TTTAAACTCC
Statistics
Matches: 410, Mismatches: 76, Indels: 92
0.71 0.13 0.16
Matches are distributed among these distances:
27 66 0.16
28 1 0.00
29 1 0.00
31 1 0.00
32 56 0.14
33 81 0.20
34 149 0.36
35 11 0.03
36 6 0.01
37 1 0.00
39 1 0.00
40 3 0.01
41 1 0.00
42 2 0.00
43 1 0.00
44 2 0.00
45 1 0.00
46 1 0.00
47 1 0.00
49 4 0.01
50 20 0.05
ACGTcount: A:0.22, C:0.31, G:0.10, T:0.36
Consensus pattern (33 bp):
CCTTTTAAGTCCACAACTCCATGGCACCTTTTT
Found at i:21296 original size:34 final size:33
Alignment explanation
Indices: 21231--21419 Score: 197
Period size: 33 Copynumber: 5.7 Consensus size: 33
21221 TCCATGGCCC
* * *
21231 CCATAACTCTGTGGCACTTTTTTTCC-CTTAAGT
1 CCATAACTCAGTGGCAC-CTTTTTCCTTTTAAGT
* *
21264 CCACAACTCAGTGGCGCCCTTTTTCCTTTTAAGT
1 CCATAACTCAGTGGC-ACCTTTTTCCTTTTAAGT
* *
21298 CCATAACTTC-GTGGCACCTTTTTCCCTTTAAAT
1 CCATAAC-TCAGTGGCACCTTTTTCCTTTTAAGT
* *
21331 CCATAACTCAATGGCACCTTTTTTCCTTTTAAAT
1 CCATAACTCAGTGGCACC-TTTTTCCTTTTAAGT
* * *
21365 CCATAATTCTGTGGCACC-TTTTCCTTTCAAGT
1 CCATAACTCAGTGGCACCTTTTTCCTTTTAAGT
21397 CCATAACTCTA-TGGCACCTTTTT
1 CCATAACTC-AGTGGCACCTTTTT
21420 AAATCCACAA
Statistics
Matches: 131, Mismatches: 18, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
32 29 0.22
33 53 0.40
34 47 0.36
35 2 0.02
ACGTcount: A:0.21, C:0.29, G:0.11, T:0.40
Consensus pattern (33 bp):
CCATAACTCAGTGGCACCTTTTTCCTTTTAAGT
Found at i:21326 original size:118 final size:118
Alignment explanation
Indices: 21131--21345 Score: 312
Period size: 118 Copynumber: 1.8 Consensus size: 118
21121 CCATGGCACC
21131 TTTTTCCCTTGAAGTCAGCAACTCAATGGCACCCTTTTTCCTTTTAAGTCCATAATTCTATGGCA
1 TTTTTCCCTTGAAGTCAGCAACTCAATGGCACCCTTTTTCCTTTTAAGTCCATAATTCTATGGCA
* *
21196 CCTTTCTTCCTTTTAAGTCCACAACTCCATGGCCCCCATAACTCTGTGGCACTT
66 CCTTTCTTCC-TTTAAATCCACAACTCAATGGCCCCCATAACTCTGTGGCACTT
* * *
21250 TTTTTCCCTT-AAGTCCA-CAACTCAGTGGCGCCCTTTTTCCTTTTAAGTCCATAACTTC-GTGG
1 TTTTTCCCTTGAAGT-CAGCAACTCAATGGCACCCTTTTTCCTTTTAAGTCCATAA-TTCTATGG
*
21312 CACCTTT-TTCCCTTTAAATCCATAACTCAATGGC
64 CACCTTTCTT-CCTTTAAATCCACAACTCAATGGC
21346 ACCTTTTTTC
Statistics
Matches: 87, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
117 21 0.24
118 51 0.59
119 15 0.17
ACGTcount: A:0.21, C:0.31, G:0.12, T:0.37
Consensus pattern (118 bp):
TTTTTCCCTTGAAGTCAGCAACTCAATGGCACCCTTTTTCCTTTTAAGTCCATAATTCTATGGCA
CCTTTCTTCCTTTAAATCCACAACTCAATGGCCCCCATAACTCTGTGGCACTT
Found at i:21339 original size:67 final size:68
Alignment explanation
Indices: 21231--21419 Score: 239
Period size: 67 Copynumber: 2.9 Consensus size: 68
21221 TCCATGGCCC
* * * *
21231 CCATAAC-TCTGTGGCACTTTTTTTCCC-TTAAGTCCACAACTCAGTGGCGCCCTTTTTCCTTTT
1 CCATAACTTCTGTGGCAC-CTTTTTCCCTTTAAGTCCATAACTCAATGGCACCCTTTTTCCTTTT
*
21294 AAGT
65 AAAT
* *
21298 CCATAACTTC-GTGGCACCTTTTTCCCTTTAAATCCATAACTCAATGGCACCTTTTTTCCTTTTA
1 CCATAACTTCTGTGGCACCTTTTTCCCTTTAAGTCCATAACTCAATGGCACCCTTTTTCCTTTTA
21362 AAT
66 AAT
*
21365 CCATAA-TTCTGTGGCACC-TTTT-CCTTTCAAGTCCATAACTCTATGGCA-CCTTTTT
1 CCATAACTTCTGTGGCACCTTTTTCCCTTT-AAGTCCATAACTCAATGGCACCCTTTTT
21420 AAATCCACAA
Statistics
Matches: 108, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
65 11 0.10
66 33 0.31
67 62 0.57
68 2 0.02
ACGTcount: A:0.21, C:0.29, G:0.11, T:0.40
Consensus pattern (68 bp):
CCATAACTTCTGTGGCACCTTTTTCCCTTTAAGTCCATAACTCAATGGCACCCTTTTTCCTTTTA
AAT
Found at i:21463 original size:93 final size:95
Alignment explanation
Indices: 21324--21509 Score: 238
Period size: 93 Copynumber: 2.0 Consensus size: 95
21314 CCTTTTTCCC
* * * *
21324 TTTAAATCCATAACTCAATGGCACCTTTTTTCCTTTTAAATCCATAA-TTCTGTGGCAC-CTTT-
1 TTTAAATCCACAAATCAATGGCACCTTTTTTCCTTTTAAACCCATAATTTC-GTGACACTCTTTC
* *
21386 TCCTTTCAAGTCCATAACTCTATGGCACCTT
65 ACCTTTCAAGTCCACAACTCTATGGCACCTT
*
21417 TTTAAATCCACAAATCCATGGCACC-TTTTT-CTTTTCAAAGCCCATAATTTCGTGACACTCTTT
1 TTTAAATCCACAAATCAATGGCACCTTTTTTCCTTTT-AAA-CCCATAATTTCGTGACACTCTTT
*
21480 CACCTTTTAAGTCCACAACTCTATGGCACC
64 CACCTTTCAAGTCCACAACTCTATGGCACC
21510 CATTTTGCTT
Statistics
Matches: 80, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
91 5 0.06
92 8 0.10
93 34 0.43
94 7 0.09
95 26 0.32
ACGTcount: A:0.26, C:0.28, G:0.09, T:0.37
Consensus pattern (95 bp):
TTTAAATCCACAAATCAATGGCACCTTTTTTCCTTTTAAACCCATAATTTCGTGACACTCTTTCA
CCTTTCAAGTCCACAACTCTATGGCACCTT
Found at i:21558 original size:27 final size:27
Alignment explanation
Indices: 21517--21620 Score: 109
Period size: 27 Copynumber: 3.7 Consensus size: 27
21507 ACCCATTTTG
*
21517 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
21544 CTTTTATGTCTACAACTCCGTGGCACATTTTC
1 CTTTTAAGTCCACAACTCCGTGGCAC-----C
* * *
21576 CTTCTAAGTCCACATCTCCATGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
21603 CTTTTAAGTCCACAACTC
1 CTTTTAAGTCCACAACTC
21621 TATGCCACCA
Statistics
Matches: 62, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
27 40 0.65
32 22 0.35
ACGTcount: A:0.22, C:0.34, G:0.12, T:0.33
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:21629 original size:27 final size:27
Alignment explanation
Indices: 21517--21634 Score: 83
Period size: 27 Copynumber: 4.2 Consensus size: 27
21507 ACCCATTTTG
** *
21517 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCATGCCACC
* * * *
21544 CTTTTATGTCTACAACTCCGTGGCACATTTTC
1 CTTTTAAGTCCACAACTCCAT-GC-CA---CC
* * *
21576 CTTCTAAGTCCACATCTCCATGGCACC
1 CTTTTAAGTCCACAACTCCATGCCACC
*
21603 CTTTTAAGTCCACAACTCTATGCCACC
1 CTTTTAAGTCCACAACTCCATGCCACC
*
21630 ATTTT
1 CTTTT
21635 CCCTTTAACA
Statistics
Matches: 69, Mismatches: 17, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
27 46 0.67
28 1 0.01
29 2 0.03
30 2 0.03
31 1 0.01
32 17 0.25
ACGTcount: A:0.22, C:0.33, G:0.11, T:0.34
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCATGCCACC
Found at i:21665 original size:59 final size:59
Alignment explanation
Indices: 21482--21667 Score: 214
Period size: 59 Copynumber: 3.1 Consensus size: 59
21472 CACTCTTTCA
*
21482 CCTTTTAAGTCCACAACTCTATGGCACCCATTTTGCTTTTAAGTCCACAACTCTGTGGCAC
1 CCTTTTAAGTCCACAACTCTATGGCA-CCATTTT-CCTTTAAGTCCACAACTCTGTGGCAC
* * ** * **
21543 CCTTTTATGTCTACAACTCCGTGGCA-CATTTTCCTTCTAAGTCCACATCTCCATGGCAC
1 CCTTTTAAGTCCACAACTCTATGGCACCATTTTCCTT-TAAGTCCACAACTCTGTGGCAC
* *
21602 CCTTTTAAGTCCACAACTCTATGCCACCATTTTCCCTTTAACAT-CACAACTCTGTGGCAC
1 CCTTTTAAGTCCACAACTCTATGGCACCATTTT-CCTTTAA-GTCCACAACTCTGTGGCAC
*
21662 CTTTTT
1 CCTTTT
21668 TTTAAACTCC
Statistics
Matches: 103, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
58 3 0.03
59 46 0.45
60 27 0.26
61 27 0.26
ACGTcount: A:0.22, C:0.33, G:0.11, T:0.34
Consensus pattern (59 bp):
CCTTTTAAGTCCACAACTCTATGGCACCATTTTCCTTTAAGTCCACAACTCTGTGGCAC
Found at i:21780 original size:33 final size:32
Alignment explanation
Indices: 21705--21807 Score: 129
Period size: 32 Copynumber: 3.2 Consensus size: 32
21695 CATCCCTTCA
* * *
21705 AAAGCCCACACAAGTTGATGGCAACCCTACTT
1 AAAGCCCACATAAGTTGGTGGCAACCCTTCTT
21737 AAAGCCCACATAAGTTGGTGGCAACCCTTCTCT
1 AAAGCCCACATAAGTTGGTGGCAACCCTTCT-T
* * *
21770 AAAGCTCACATAAGTCGGTGGCAACTCTTC-T
1 AAAGCCCACATAAGTTGGTGGCAACCCTTCTT
21801 AAA-CCCA
1 AAAGCCCA
21808 ATGTCGCTGG
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
30 3 0.05
31 4 0.06
32 28 0.44
33 28 0.44
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (32 bp):
AAAGCCCACATAAGTTGGTGGCAACCCTTCTT
Found at i:21995 original size:49 final size:49
Alignment explanation
Indices: 21805--22097 Score: 277
Period size: 49 Copynumber: 6.0 Consensus size: 49
21795 TCTTCTAAAC
** * *
21805 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-TCGATCTTTATGT
1 CCAATGTCGCTGGCCTTGAATCAAAACATTAGCACCTTC-ATCTTTAAGT
* * * * * ** * *
21854 CCAATGCCGCTAGCCCTAAATTAGCATATCAGCACCTTCATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAAAACATTAGCACCTTCATCTTTAAGT
* *
21903 CCAAGGTCGCTGGCCTTGAATC-AAACATTAGCACC-TCTATCTTTATGT
1 CCAATGTCGCTGGCCTTGAATCAAAACATTAGCACCTTC-ATCTTTAAGT
* * *
21951 CTAATGTCGCTGGCCTTGAAACAAAACATTAGCACCTTCATCTTTAAAT
1 CCAATGTCGCTGGCCTTGAATCAAAACATTAGCACCTTCATCTTTAAGT
* * * * * *
22000 CCAATGTTGCTGGCCTTGAATTAACACGTTGGCACCTTCACCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAAAACATTAGCACCTTCATCTTTAAGT
* ** ** *
22049 CTAATGTCATTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAAAACATTAGCACCTTCATCTTTAAGT
22098 TCGATATGGC
Statistics
Matches: 198, Mismatches: 42, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
47 2 0.01
48 37 0.19
49 155 0.78
50 4 0.02
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.31
Consensus pattern (49 bp):
CCAATGTCGCTGGCCTTGAATCAAAACATTAGCACCTTCATCTTTAAGT
Found at i:22078 original size:98 final size:98
Alignment explanation
Indices: 21795--22095 Score: 345
Period size: 98 Copynumber: 3.1 Consensus size: 98
21785 CGGTGGCAAC
* * *
21795 TCTTCTAAACCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTCGATCTTTATGTCCAATG
1 TCTT-TAAATCCAATGTCGCTGGCCTTGAATCAACACATTGGCACCTCGATCTTTATGTCTAATG
* * * * * * *
21860 CCGCTAGCCCTAAATTAGCATATCAGCACCTTCA
65 TCGCTGGCCTTGAATCAGCACATTAGCACCTTCA
* * * *
21894 TCTTTAAGTCCAAGGTCGCTGGCCTTGAATCAA-ACATTAGCACCTCTATCTTTATGTCTAATGT
1 TCTTTAAATCCAATGTCGCTGGCCTTGAATCAACACATTGGCACCTCGATCTTTATGTCTAATGT
* **
21958 CGCTGGCCTTGAAACAAAACATTAGCACCTTCA
66 CGCTGGCCTTGAATCAGCACATTAGCACCTTCA
* * * * *
21991 TCTTTAAATCCAATGTTGCTGGCCTTGAATTAACACGTTGGCACCTTC-ACCTTTAAGTCTAATG
1 TCTTTAAATCCAATGTCGCTGGCCTTGAATCAACACATTGGCACC-TCGATCTTTATGTCTAATG
** *
22055 TCATTGGCCTTGAATCAGCACATTGGCACCTTCA
65 TCGCTGGCCTTGAATCAGCACATTAGCACCTTCA
22089 TCTTTAA
1 TCTTTAA
22096 GTTCGATATG
Statistics
Matches: 169, Mismatches: 31, Indels: 5
0.82 0.15 0.02
Matches are distributed among these distances:
97 80 0.47
98 83 0.49
99 6 0.04
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.32
Consensus pattern (98 bp):
TCTTTAAATCCAATGTCGCTGGCCTTGAATCAACACATTGGCACCTCGATCTTTATGTCTAATGT
CGCTGGCCTTGAATCAGCACATTAGCACCTTCA
Found at i:22119 original size:49 final size:49
Alignment explanation
Indices: 21813--22135 Score: 208
Period size: 49 Copynumber: 6.6 Consensus size: 49
21803 ACCCAATGTC
* * ***
21813 GCTGGCCTTGAATCAGCACATTGGCACC-TCGATCTTTATGTCCAATGCC
1 GCTGGCCTTGAATCAGCACATTGGCACCTTC-ATCTTTAAGTTCAATATG
* * * * * ** * ** *
21862 GCTAGCCCTAAATTAGCATATCAGCACCTTCATCTTTAAGTCCAAGGTC
1 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTTCAATATG
* * * * *
21911 GCTGGCCTTGAATCA-AACATTAGCACC-TCTATCTTTATG-TCTAATGTC
1 GCTGGCCTTGAATCAGCACATTGGCACCTTC-ATCTTTAAGTTC-AATATG
* ** * * * * *
21959 GCTGGCCTTGAAACAAAACATTAGCACCTTCATCTTTAAATCCAATGTT
1 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTTCAATATG
* * * * *
22008 GCTGGCCTTGAATTAACACGTTGGCACCTTCACCTTTAAG-TCTA-ATG
1 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTTCAATATG
* *
22055 TCATTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTTCGATATG
1 GC--TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTTCAATATG
* * *
22106 GCTAGCCTGGAATCAGCATATTGGCACCTT
1 GCTGGCCTTGAATCAGCACATTGGCACCTT
22136 TAACATTCCT
Statistics
Matches: 218, Mismatches: 46, Indels: 20
0.77 0.16 0.07
Matches are distributed among these distances:
47 5 0.02
48 38 0.17
49 163 0.75
50 8 0.04
51 4 0.02
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.31
Consensus pattern (49 bp):
GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTTCAATATG
Found at i:22130 original size:98 final size:98
Alignment explanation
Indices: 21884--22135 Score: 247
Period size: 98 Copynumber: 2.6 Consensus size: 98
21874 TTAGCATATC
* ** * * * * *
21884 AGCACCTTCATCTTTAAGTCCAAGGTCGCTGGCCTTGAATCAA-ACATTAGCACC-TCTATCTTT
1 AGCACCTTCATCTTTAAATCCAATATGGCTAGCCTGGAATCAACACATTGGCACCTTC-ACCTTT
* *
21947 ATGTCTAATGTCGCTGGCCTTGAAACAAAACATT
65 AAGTCTAATGTCACTGGCCTTGAAACAAAACATT
* * * * * *
21981 AGCACCTTCATCTTTAAATCCAATGTTGCTGGCCTTGAATTAACACGTTGGCACCTTCACCTTTA
1 AGCACCTTCATCTTTAAATCCAATATGGCTAGCCTGGAATCAACACATTGGCACCTTCACCTTTA
* * **
22046 AGTCTAATGTCATTGGCCTTGAATCAGCACATT
66 AGTCTAATGTCACTGGCCTTGAAACAAAACATT
* * * * * *
22079 GGCACCTTCATCTTTAAGTTCGATATGGCTAGCCTGGAATCAGCATATTGGCACCTT
1 AGCACCTTCATCTTTAAATCCAATATGGCTAGCCTGGAATCAACACATTGGCACCTT
22136 TAACATTCCT
Statistics
Matches: 128, Mismatches: 25, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
97 39 0.30
98 87 0.68
99 2 0.02
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (98 bp):
AGCACCTTCATCTTTAAATCCAATATGGCTAGCCTGGAATCAACACATTGGCACCTTCACCTTTA
AGTCTAATGTCACTGGCCTTGAAACAAAACATT
Found at i:22208 original size:52 final size:52
Alignment explanation
Indices: 22152--22252 Score: 130
Period size: 52 Copynumber: 1.9 Consensus size: 52
22142 TCCTAAGGCC
* * * *
22152 AATGTCGCTAGCCTTAAATTAGCACATTGGCATTCTTCTCATCTTTAAGTCT
1 AATGTCGCTAGCCGTAAATCAGCACATTAGCATTCTTCGCATCTTTAAGTCT
* * * *
22204 AATGTCGTTGGTCGTGAATCAGCACATTAGCATTCTTCGCATCTTTAAG
1 AATGTCGCTAGCCGTAAATCAGCACATTAGCATTCTTCGCATCTTTAAG
22253 CGCAATATCG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 41 1.00
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.37
Consensus pattern (52 bp):
AATGTCGCTAGCCGTAAATCAGCACATTAGCATTCTTCGCATCTTTAAGTCT
Found at i:22268 original size:52 final size:52
Alignment explanation
Indices: 22172--22287 Score: 144
Period size: 52 Copynumber: 2.2 Consensus size: 52
22162 GCCTTAAATT
* * * * *
22172 AGCACATTGGCATTCTTCTCATCTTTAAGTCTAATGTCGTTGGTCGTGAATC
1 AGCACATTAGCATTCTTCGCATCTTTAAGTCCAATATCGCTGGTCGTGAATC
* *
22224 AGCACATTAGCATTCTTCGCATCTTTAAG-CGCAATATCGCTGGTCTTGAATT
1 AGCACATTAGCATTCTTCGCATCTTTAAGTC-CAATATCGCTGGTCGTGAATC
*
22276 AGCATATTAGCA
1 AGCACATTAGCA
22288 CCTTTATCAT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
51 1 0.02
52 54 0.98
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (52 bp):
AGCACATTAGCATTCTTCGCATCTTTAAGTCCAATATCGCTGGTCGTGAATC
Found at i:22370 original size:18 final size:17
Alignment explanation
Indices: 22347--22380 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
22337 AGTATACTGG
*
22347 CATCTTTATCACTCTTCT
1 CATCTTCATCA-TCTTCT
22365 CATCTTCATCATCTTC
1 CATCTTCATCATCTTC
22381 AAGTCCAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.18, C:0.35, G:0.00, T:0.47
Consensus pattern (17 bp):
CATCTTCATCATCTTCT
Found at i:22370 original size:61 final size:61
Alignment explanation
Indices: 22237--22370 Score: 151
Period size: 61 Copynumber: 2.2 Consensus size: 61
22227 ACATTAGCAT
* * ** * * * *
22237 TCTTCGCATCTTTAAGCGCAATATCGCTGGTCTTGAATTAGCATATTAGCACCTTTATCAT
1 TCTTCTCATCTTTAAGCCCAATATCGCAAGCCTTGAATCAGCATACTAGCACCTTTATCAC
* * * * *
22298 TTTTCTTATCTTTAAGCCCAATATCGCAAGCCTTGAATCAGTATACTGGCATCTTTATCAC
1 TCTTCTCATCTTTAAGCCCAATATCGCAAGCCTTGAATCAGCATACTAGCACCTTTATCAC
22359 TCTTCTCATCTT
1 TCTTCTCATCTT
22371 CATCATCTTC
Statistics
Matches: 58, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.40
Consensus pattern (61 bp):
TCTTCTCATCTTTAAGCCCAATATCGCAAGCCTTGAATCAGCATACTAGCACCTTTATCAC
Found at i:23085 original size:19 final size:21
Alignment explanation
Indices: 23037--23089 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
23027 AATTTCTATA
23037 ATTTGTATCGATACAAATAGT
1 ATTTGTATCGATACAAATAGT
** *
23058 AAATGTATCGATACATA-AGT
1 ATTTGTATCGATACAAATAGT
23078 -TTTGTATCGATA
1 ATTTGTATCGATA
23090 TAATGTATCG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 10 0.37
20 3 0.11
21 14 0.52
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (21 bp):
ATTTGTATCGATACAAATAGT
Found at i:28603 original size:20 final size:21
Alignment explanation
Indices: 28580--28618 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
28570 CAAAGCAATA
28580 TGTATCGATAC-TTCTAGGCT
1 TGTATCGATACTTTCTAGGCT
28600 TGTATCGATACTTTCTAGG
1 TGTATCGATACTTTCTAGG
28619 GTTTTGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (21 bp):
TGTATCGATACTTTCTAGGCT
Found at i:33198 original size:79 final size:78
Alignment explanation
Indices: 33085--33500 Score: 400
Period size: 79 Copynumber: 5.3 Consensus size: 78
33075 TATTTTGGAG
* * * *
33085 ATAATAACGGGGTTGGAGTATCCCTTC-GAAAATAACAGGGTTGGAGTATCCTCGATTGTGAAAA
1 ATAA-AACCGGGTTGGAGTATCCCCTCAG-AAATAACAGGGTTGGAGTATCCCCGATTATGAAAA
*
33149 ATCGATGATTTAGAA
64 ATTGATGATTTAGAA
* *
33164 ATAAAACCGGGATTGGAATATCCCCTCAGAAATAAC-GAGGTTGGAGTATCCCCGACTATGAAAA
1 ATAAAACCGGG-TTGGAGTATCCCCTCAGAAATAACAG-GGTTGGAGTATCCCCGATTATGAAAA
*
33228 ATTGATGTTTTAGAA
64 ATTGATGATTTAGAA
* ** *
33243 ATAAAACCGAGGTTGGAGTATTCCCTCAGAAATAATGGGGTTGGAGTATCCCCGATTATGAGAAA
1 ATAAAACCG-GGTTGGAGTATCCCCTCAGAAATAACAGGGTTGGAGTATCCCCGATTATGAAAAA
*
33308 TTAAT-ATTTTAGAA
65 TTGATGA-TTTAGAA
* * ** *
33322 ATAAAGCCGGGGTTGGGGTATCCTTTGA-AAATAACAGGGTTGGAGTATCCCCG---ATGAAAAA
1 ATAAAACC-GGGTTGGAGTATCCCCTCAGAAATAACAGGGTTGGAGTATCCCCGATTATGAAAAA
*
33383 TTGATGTTTTAGAA
65 TTGATGATTTAGAA
* * * * * *
33397 ATAAAACAAGGGTTGGATTGTCCCCTC-GAAAATAACGGGGTTGGAGTATCCCCGAATATGGAAA
1 ATAAAAC-CGGGTTGGAGTATCCCCTCAG-AAATAACAGGGTTGGAGTATCCCCGATTATGAAAA
**
33461 A-TGGGGATTTTAGAA
64 ATTGATGA-TTTAGAA
** *
33476 ATAAAATAAGAGTTGGAGTATCCCC
1 ATAAAA-CCGGGTTGGAGTATCCCC
33501 GATTAAGAAA
Statistics
Matches: 278, Mismatches: 43, Indels: 32
0.79 0.12 0.09
Matches are distributed among these distances:
75 36 0.13
76 24 0.09
78 33 0.12
79 180 0.65
80 5 0.02
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.27
Consensus pattern (78 bp):
ATAAAACCGGGTTGGAGTATCCCCTCAGAAATAACAGGGTTGGAGTATCCCCGATTATGAAAAAT
TGATGATTTAGAA
Found at i:33431 original size:154 final size:155
Alignment explanation
Indices: 33085--33460 Score: 449
Period size: 158 Copynumber: 2.4 Consensus size: 155
33075 TATTTTGGAG
* * * * * *
33085 ATAATAACGGGGTTGGAGTATCCCTTCGAAAATAACAGGGTTGGAGTATCCTCGATTGTGAAAAA
1 ATAA-AACAGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAA
*
33150 TCGATGATTTAGAAATAAAACCGGGATTGGAATATCCCCTCAGAAATAACGAGGTTGGAGTATCC
65 TCAATGATTTAGAAATAAAACCGGGATTGGAATATCCCCTCAGAAATAACGAGGTTGGAGTATCC
33215 CCGACTATGAAAAATTGATGTTTTAGAA
130 CCGA--ATGAAAAATTGATGTTTTAGAA
* * *
33243 ATAAAACCGAGGTTGGAGTATTCCCTC-AGAAATAATGGGGTTGGAGTATCCCCGATTATGAGAA
1 ATAAAACAG-GGTTGGAGTATCCCCTCGA-AAATAACGGGGTTGGAGTATCCCCGATTATGAGAA
* * * ** ** *
33307 ATTAAT-ATTTTAGAAATAAAGCCGGGGTTGGGGTATCCTTTGA-AAATAAC-AGGGTTGGAGTA
64 ATCAATGA-TTTAGAAATAAAACCGGGATTGGAATATCCCCTCAGAAATAACGA-GGTTGGAGTA
33369 TCCCCG-ATGAAAAATTGATGTTTTAGAA
127 TCCCCGAATGAAAAATTGATGTTTTAGAA
* * *
33397 ATAAAACAAGGGTTGGATTGTCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAATATG-GAAA
1 ATAAAAC-AGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAA
33461 ATGGGGATTT
Statistics
Matches: 189, Mismatches: 23, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
153 4 0.02
154 72 0.38
155 2 0.01
156 1 0.01
157 29 0.15
158 81 0.43
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.27
Consensus pattern (155 bp):
ATAAAACAGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAAT
CAATGATTTAGAAATAAAACCGGGATTGGAATATCCCCTCAGAAATAACGAGGTTGGAGTATCCC
CGAATGAAAAATTGATGTTTTAGAA
Found at i:33476 original size:154 final size:155
Alignment explanation
Indices: 33085--33481 Score: 455
Period size: 154 Copynumber: 2.5 Consensus size: 155
33075 TATTTTGGAG
* * * * * *
33085 ATAATAACGGGGTTGGAGTATCCCTTCGAAAATAACAGGGTTGGAGTATCCTCGATTGTGAAAAA
1 ATAA-AACAGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGGAAAA
*
33150 TCGATGA-TTTAGAAATAAAACCGGGATTGGAATATCCCCTCAGAAATAACGAGGTTGGAGTATC
65 T-GAAGATTTTAGAAATAAAACCGGGATTGGAATATCCCCTCAGAAATAACGAGGTTGGAGTATC
33214 CCCGACTATGAAAAATTGATGTTTTAGAA
129 CCCGA--ATGAAAAATTGATGTTTTAGAA
* * *
33243 ATAAAACCGAGGTTGGAGTATTCCCTC-AGAAATAATGGGGTTGGAGTATCCCCGATTAT-GAGA
1 ATAAAACAG-GGTTGGAGTATCCCCTCGA-AAATAACGGGGTTGGAGTATCCCCGATTATGGA-A
* * * * ** ** *
33306 AATTAATATTTTAGAAATAAAGCCGGGGTTGGGGTATCCTTTGA-AAATAAC-AGGGTTGGAGTA
63 AATGAAGATTTTAGAAATAAAACCGGGATTGGAATATCCCCTCAGAAATAACGA-GGTTGGAGTA
33369 TCCCCG-ATGAAAAATTGATGTTTTAGAA
127 TCCCCGAATGAAAAATTGATGTTTTAGAA
* * *
33397 ATAAAACAAGGGTTGGATTGTCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAATATGGAAAA
1 ATAAAAC-AGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGGAAAA
**
33462 TGGGGATTTTAGAAATAAAA
65 TGAAGATTTTAGAAATAAAA
33482 TAAGAGTTGG
Statistics
Matches: 202, Mismatches: 29, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
154 89 0.44
155 4 0.02
156 1 0.00
157 31 0.15
158 77 0.38
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (155 bp):
ATAAAACAGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGGAAAAT
GAAGATTTTAGAAATAAAACCGGGATTGGAATATCCCCTCAGAAATAACGAGGTTGGAGTATCCC
CGAATGAAAAATTGATGTTTTAGAA
Found at i:34025 original size:34 final size:35
Alignment explanation
Indices: 33987--34053 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
33977 CCTTACAACA
33987 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
34021 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
34054 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:34530 original size:13 final size:13
Alignment explanation
Indices: 34512--34537 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34502 CAATTTTTTG
34512 TGTATCGATACAT
1 TGTATCGATACAT
34525 TGTATCGATACAT
1 TGTATCGATACAT
34538 ACTTTGTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:34549 original size:32 final size:33
Alignment explanation
Indices: 34492--34555 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
34482 TACAAGCCAA
**
34492 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
34525 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
34556 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:35276 original size:21 final size:21
Alignment explanation
Indices: 35233--35278 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
35223 TAATTCACGC
* *
35233 ATTCTCCCCCGTTTATTAATA
1 ATTCTCCCCCGTTAATCAATA
35254 ATTCTCCCCC-TTAATCAAGTA
1 ATTCTCCCCCGTTAATCAA-TA
35275 ATTC
1 ATTC
35279 ATATCAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.26, C:0.30, G:0.04, T:0.39
Consensus pattern (21 bp):
ATTCTCCCCCGTTAATCAATA
Found at i:35706 original size:30 final size:31
Alignment explanation
Indices: 35650--35717 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 31
35640 TTCATGCAAC
* * *
35650 TAATACCAAAAGTTTATGCAAGCTCTCCCCCT
1 TAATA-CAAAAGTTTATACAAACTCTCCCCCA
35682 TAATACAAAA-TTTATACAAACTCTCCCCCA
1 TAATACAAAAGTTTATACAAACTCTCCCCCA
35712 TAATAC
1 TAATAC
35718 GTTGTCACCC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 23 0.70
31 5 0.15
32 5 0.15
ACGTcount: A:0.38, C:0.29, G:0.04, T:0.28
Consensus pattern (31 bp):
TAATACAAAAGTTTATACAAACTCTCCCCCA
Found at i:36549 original size:13 final size:13
Alignment explanation
Indices: 36531--36557 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
36521 ACTGAAGTAA
36531 TGTATCGATACAT
1 TGTATCGATACAT
36544 TGTATCGATACAT
1 TGTATCGATACAT
36557 T
1 T
36558 CTGGAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:40312 original size:13 final size:13
Alignment explanation
Indices: 40294--40319 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40284 CAATTTTTTG
40294 TGTATCGATACAT
1 TGTATCGATACAT
40307 TGTATCGATACAT
1 TGTATCGATACAT
40320 ACTTTGTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:40331 original size:32 final size:33
Alignment explanation
Indices: 40274--40337 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
40264 TACAAGCCAA
**
40274 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
40307 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
40338 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Done.