Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1044
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: 10397
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Found at i:2591 original size:31 final size:30
Alignment explanation
Indices: 2554--2713 Score: 182
Period size: 31 Copynumber: 5.2 Consensus size: 30
2544 AATTCTTCAA
* *
2554 ATCTCTTCTCAAAGCCCACGACTCAGTGGC
1 ATCTTTTCTCAAAGTCCACGACTCAGTGGC
*
2584 AATCTCTTCTCAAAGTCCACGACTCAGTGGC
1 -ATCTTTTCTCAAAGTCCACGACTCAGTGGC
2615 ATCTTTTTCTTCAAAGTCCACGACTCAGTGGC
1 ATC-TTTTC-TCAAAGTCCACGACTCAGTGGC
2647 AT-TTTGTCTCAAAGTCCACGACTCA-TGGC
1 ATCTTT-TCTCAAAGTCCACGACTCAGTGGC
* * *
2676 ATCCTTTTCTTC-AAGCCCACAACTCCGTGGC
1 AT-CTTTTC-TCAAAGTCCACGACTCAGTGGC
*
2707 ACCTTTT
1 ATCTTTT
2714 TCTTTTTAAA
Statistics
Matches: 116, Mismatches: 6, Indels: 15
0.85 0.04 0.11
Matches are distributed among these distances:
29 6 0.05
30 41 0.35
31 45 0.39
32 24 0.21
ACGTcount: A:0.23, C:0.33, G:0.15, T:0.30
Consensus pattern (30 bp):
ATCTTTTCTCAAAGTCCACGACTCAGTGGC
Found at i:2739 original size:93 final size:93
Alignment explanation
Indices: 2560--2740 Score: 217
Period size: 92 Copynumber: 1.9 Consensus size: 93
2550 TCAAATCTCT
* * *
2560 TCTCAAAGCCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCATCTTTTTCT
1 TCTCAAAGCCCACGACTCAGTGGCAATCTCTTCTCAAAGCCCACAACTCAGTGGCACCTTTTTCT
*
2625 TCAAAGTCCACGACTCAGTGGCATTTTG
66 TCAAAGCCCACGACTCAGTGGCATTTTG
* * *
2653 TCTCAAAGTCCACGACTCA-TGGC-ATCCTTTTCTTC-AAGCCCACAACTCCGTGGCACCTTTTT
1 TCTCAAAGCCCACGACTCAGTGGCAAT-CTCTTC-TCAAAGCCCACAACTCAGTGGCACCTTTTT
* *
2715 CTTTTTAAAGCCCAC-ACTCCGTGGCA
64 C--TTCAAAGCCCACGACTCAGTGGCA
2741 CTCTTTTTCC
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
91 2 0.03
92 33 0.44
93 30 0.40
94 10 0.13
ACGTcount: A:0.23, C:0.33, G:0.15, T:0.29
Consensus pattern (93 bp):
TCTCAAAGCCCACGACTCAGTGGCAATCTCTTCTCAAAGCCCACAACTCAGTGGCACCTTTTTCT
TCAAAGCCCACGACTCAGTGGCATTTTG
Found at i:2769 original size:35 final size:34
Alignment explanation
Indices: 2688--3256 Score: 447
Period size: 33 Copynumber: 17.3 Consensus size: 34
2678 CCTTTTCTTC
*
2688 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTTA
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTTA
2722 AAGCCCAC-ACTCCGTGGCACTCTTTTTCCCTTTT-
1 AAGCCCACAACTCCGTGGCAC-CTTTTT-CCTTTTA
* *
2756 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTT-
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTTA
* * *
2789 AAGTCCACGACTCCGTGGCACC---TT-CTTTTC
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTTA
* * *
2819 AAGCCCACCAATTTCGTGGCAACCTTTTT-CTTCTCA
1 AAGCCCA-CAACTCCGTGGC-ACCTTTTTCCTT-TTA
* *
2855 AAGCCCACCACTCCGTGGCA-CTTTTTCTTTTTA
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTTA
*
2888 AAGCCCACAACTCCGTGACACTCTTTTTCCCTTTTCA
1 AAGCCCACAACTCCGTGGCAC-CTTTTT-CCTTTT-A
* * *
2925 AAGCCCACCACTCTGTGGCA-CTTTTTCTTTTTA
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTTA
2958 AAGCCCACAAACTCCGTGGCACTCTTTTTCCCTTTTCA
1 AAGCCCAC-AACTCCGTGGCAC-CTTTTT-CCTTTT-A
*
2996 AAGCCCACAACTCCATGGCACTCTTTTTCCCTTTTA
1 AAGCCCACAACTCCGTGGCAC-CTTTTT-CCTTTTA
* * * *
3032 AAGTCCACGACTTCGTGGCACC---TT-CTTTTC
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTTA
3062 AAGCCCACAACT-CGTGGCA-C-----CCTTTT-
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTTA
* *
3088 AAGCCCACAACTCCCGTGGCACTTTTTTCATCTTT-
1 AAGCCCACAACT-CCGTGGCACCTTTTTCCT-TTTA
* *
3123 AAGTCCACAACTCTGTGGC-CAC-----CCTTTTA
1 AAGCCCACAACTCCGTGGCAC-CTTTTTCCTTTTA
* *
3152 AAGCCCACAACTCCGTGGCACTTTTTTTCATCTTT-
1 AAGCCCACAACTCCGTGGCAC-CTTTTTCCT-TTTA
*
3187 AAGTCCACAACTCCGTGGCA-C-----CCTTTT-
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTTA
* *
3214 AAGCCCACAACTCCGTGGCACCTTTCTCCTTCTA
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTTA
3248 AAGCCCACA
1 AAGCCCACA
3257 CAAGTCGGTG
Statistics
Matches: 440, Mismatches: 49, Indels: 92
0.76 0.08 0.16
Matches are distributed among these distances:
26 12 0.03
27 27 0.06
28 14 0.03
29 31 0.07
30 24 0.05
31 9 0.02
32 5 0.01
33 80 0.18
34 61 0.14
35 79 0.18
36 40 0.09
37 49 0.11
38 9 0.02
ACGTcount: A:0.20, C:0.35, G:0.12, T:0.32
Consensus pattern (34 bp):
AAGCCCACAACTCCGTGGCACCTTTTTCCTTTTA
Found at i:2777 original size:68 final size:68
Alignment explanation
Indices: 2688--3256 Score: 426
Period size: 64 Copynumber: 8.6 Consensus size: 68
2678 CCTTTTCTTC
*
2688 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCAC-ACTCCGTGGCACTCTTTTTCCC
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCCGTGGCAC-CTTTTT-CC
2752 TTTT-
64 TTTTA
* * * *
2756 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTT--AAGTCCACGACTCCGTGGCACC---TT-CT
1 AAGCCCACAACTCCGTGGCACCTT-TTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCCT
*
2815 TTTC
65 TTTA
* * * * *
2819 AAGCCCACCAATTTCGTGGCAACCTTTTTCTTCTCAAAGCCCACCACTCCGTGGCA-CTTTTTCT
1 AAGCCCA-CAACTCCGTGGC-ACCTTTTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCC
2883 TTTTA
64 TTTTA
* * *
2888 AAGCCCACAACTCCGTGACACTCTTTTTCCCTTTTCAAAGCCCACCACTCTGTGGCA-CTTTTTC
1 AAGCCCACAACTCCGTGGCAC-CTTTTT--CTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTC
*
2952 TTTTTA
63 CTTTTA
*
2958 AAGCCCACAAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCATGGCACTCTTTT
1 AAGCCCAC-AACTCCGTGGCAC-CTTTTT--CTTTTCAAAGCCCACAACTCCGTGGCAC-CTTTT
3023 TCCCTTTTA
61 T-CCTTTTA
* * *
3032 AAGTCCACGACTTCGTGGCACC---TTCTTTTC-AAGCCCACAACT-CGTGGCA-C-----CCTT
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCCTT
3086 TT-
66 TTA
* * *
3088 AAGCCCACAACTCCCGTGGCACTTTTTTCATCTTT--AAGTCCACAACTCTGTGGC-CAC-----
1 AAGCCCACAACT-CCGTGGCACCTTTTTC-T-TTTCAAAGCCCACAACTCCGTGGCAC-CTTTTT
3145 CCTTTTA
62 CCTTTTA
* *
3152 AAGCCCACAACTCCGTGGCACTTTTTTTCATCTTT--AAGTCCACAACTCCGTGGCA-C-----C
1 AAGCCCACAACTCCGTGGCAC-CTTTTTC-T-TTTCAAAGCCCACAACTCCGTGGCACCTTTTTC
3209 CTTTT-
63 CTTTTA
* *
3214 AAGCCCACAACTCCGTGGCACCTTTCTC-CTTCTAAAGCCCACA
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTC-AAAGCCCACA
3257 CAAGTCGGTG
Statistics
Matches: 431, Mismatches: 37, Indels: 73
0.80 0.07 0.13
Matches are distributed among these distances:
56 10 0.02
57 14 0.03
58 2 0.00
60 3 0.01
61 25 0.06
62 34 0.08
63 30 0.07
64 61 0.14
65 12 0.03
66 30 0.07
67 16 0.04
68 52 0.12
69 20 0.05
70 46 0.11
71 45 0.10
72 1 0.00
73 17 0.04
74 13 0.03
ACGTcount: A:0.20, C:0.35, G:0.12, T:0.32
Consensus pattern (68 bp):
AAGCCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCCTT
TTA
Found at i:3087 original size:27 final size:28
Alignment explanation
Indices: 3024--3235 Score: 142
Period size: 35 Copynumber: 7.1 Consensus size: 28
3014 CACTCTTTTT
* * * *
3024 CCCTTTTAAAGTCCACGACTTCGTGGCA
1 CCCTTTTCAAGCCCACAACTCCGTGGCA
3052 CCTTCTTTTCAAGCCCACAACT-CGTGGCA
1 CC--CTTTTCAAGCCCACAACTCCGTGGCA
3081 CCCTTTT-AAGCCCACAACTCCCGTGGCA
1 CCCTTTTCAAGCCCACAACT-CCGTGGCA
** * *
3109 CTTTTTTCATCTTTAAGTCCACAACTCTGTGGCCA
1 C-CCTTT--TC---AAGCCCACAACTCCGTGG-CA
*
3144 CCCTTTTAAAGCCCACAACTCCGTGGCA
1 CCCTTTTCAAGCCCACAACTCCGTGGCA
** *
3172 CTTTTTTTCATCTTTAAGTCCACAACTCCGTGGCA
1 C--CCTTT--TC---AAGCCCACAACTCCGTGGCA
3207 CCCTTTT-AAGCCCACAACTCCGTGGCA
1 CCCTTTTCAAGCCCACAACTCCGTGGCA
3234 CC
1 CC
3236 TTTCTCCTTC
Statistics
Matches: 146, Mismatches: 19, Indels: 39
0.72 0.09 0.19
Matches are distributed among these distances:
26 12 0.08
27 26 0.18
28 13 0.09
29 28 0.19
30 18 0.12
31 2 0.01
32 2 0.01
33 3 0.02
34 8 0.05
35 34 0.23
ACGTcount: A:0.21, C:0.36, G:0.14, T:0.29
Consensus pattern (28 bp):
CCCTTTTCAAGCCCACAACTCCGTGGCA
Found at i:3115 original size:28 final size:27
Alignment explanation
Indices: 3044--3178 Score: 92
Period size: 29 Copynumber: 4.6 Consensus size: 27
3034 GTCCACGACT
3044 TCGTGGCACCTTCTTTTCAAGCCCACAAC
1 TCGTGGCA-CTT-TTTTCAAGCCCACAAC
**
3073 TCGTGGCACCCTTTT-AAGCCCACAAC
1 TCGTGGCACTTTTTTCAAGCCCACAAC
*
3099 TCCCGTGGCACTTTTTTCATCTTTAAGTCCACAAC
1 T--CGTGGCAC-TTTTT--TC---AAGCCCACAAC
** *
3134 TCTGTGGCCACCCTTTTAAAGCCCACAAC
1 TC-GTGG-CACTTTTTTCAAGCCCACAAC
3163 TCCGTGGCACTTTTTT
1 T-CGTGGCACTTTTTT
3179 TCATCTTTAA
Statistics
Matches: 83, Mismatches: 11, Indels: 25
0.70 0.09 0.21
Matches are distributed among these distances:
26 12 0.14
27 4 0.05
28 16 0.19
29 26 0.31
30 1 0.01
31 1 0.01
32 1 0.01
33 1 0.01
34 7 0.08
35 14 0.17
ACGTcount: A:0.20, C:0.35, G:0.14, T:0.31
Consensus pattern (27 bp):
TCGTGGCACTTTTTTCAAGCCCACAAC
Found at i:3170 original size:91 final size:92
Alignment explanation
Indices: 2987--3172 Score: 231
Period size: 91 Copynumber: 2.0 Consensus size: 92
2977 CACTCTTTTT
*
2987 CCCTTTTCAAAGCCCACAACTCCATGGCACTCTTTTTCCCTTTTAAAGTCCACGACTTCGTGGCA
1 CCCTTTT-AAAGCCCACAACTCCATGGCACTCTTTTTCCCTTTTAAAGTCCACAACTTCGTGGCA
*
3052 CCTTCTTTTCAAGCCCACAACTCGTGGCA
65 CC-TCTTTTAAAGCCCACAACTCGTGGCA
* *
3081 CCCTTTT-AAGCCCACAACTCCCGTGGCACT-TTTTT-CATCTTT-AAGTCCACAAC-TCTGTGG
1 CCCTTTTAAAGCCCACAACT-CCATGGCACTCTTTTTCCCT-TTTAAAGTCCACAACTTC-GTGG
3141 CCACC-CTTTTAAAGCCCACAACTCCGTGGCA
63 -CACCTCTTTTAAAGCCCACAACT-CGTGGCA
3172 C
1 C
3173 TTTTTTTCAT
Statistics
Matches: 83, Mismatches: 4, Indels: 13
0.83 0.04 0.13
Matches are distributed among these distances:
90 19 0.23
91 24 0.29
92 24 0.29
93 9 0.11
94 7 0.08
ACGTcount: A:0.22, C:0.37, G:0.13, T:0.29
Consensus pattern (92 bp):
CCCTTTTAAAGCCCACAACTCCATGGCACTCTTTTTCCCTTTTAAAGTCCACAACTTCGTGGCAC
CTCTTTTAAAGCCCACAACTCGTGGCA
Found at i:3237 original size:26 final size:27
Alignment explanation
Indices: 3184--3235 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
3174 TTTTTTCATC
*
3184 TTTAAGTCCACAACTCCGTGGCACCCT
1 TTTAAGCCCACAACTCCGTGGCACCCT
3211 TTTAAGCCCACAACTCCGTGGCACC
1 TTTAAGCCCACAACTCCGTGGCACC
3236 TTTCTCCTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.23, C:0.38, G:0.15, T:0.23
Consensus pattern (27 bp):
TTTAAGCCCACAACTCCGTGGCACCCT
Found at i:3268 original size:63 final size:59
Alignment explanation
Indices: 3024--3284 Score: 244
Period size: 64 Copynumber: 4.2 Consensus size: 59
3014 CACTCTTTTT
* * * * * *
3024 CCCTTTTAAAGTCCACGACTTCGTGGCACCTTCTT--TTC-AAGCCCACAACTCGTGGCA
1 CCCTTTT-AAGCCCACAACTCCGTGGCACTTTTTTCCTTCTAAGTCCACAACTCGTGGCA
3081 CCCTTTTAAGCCCACAACTCCCGTGGCACTTTTTTCATCTT-TAAGTCCACAACTCTGTGGCCA
1 CCCTTTTAAGCCCACAACT-CCGTGGCACTTTTTTC--CTTCTAAGTCCACAACTC-GTGG-CA
3144 CCCTTTTAAAGCCCACAACTCCGTGGCACTTTTTTTCATCTT-TAAGTCCACAACTCCGTGGCA
1 CCCTTTT-AAGCCCACAACTCCGTGGCAC-TTTTTTC--CTTCTAAGTCCACAACT-CGTGGCA
* * * *
3207 CCCTTTTAAGCCCACAACTCCGTGGCACCTTTCTCCTTCTAAAGCCCACACAAGTCGGTGGCAA
1 CCCTTTTAAGCCCACAACTCCGTGGCACTTTTTTCCTTCT-AAG-TC-CACAACTC-GTGGC-A
*
3271 CCCTTCTAAGCCCA
1 CCCTTTTAAGCCCA
3285 ATATCGCTGG
Statistics
Matches: 176, Mismatches: 11, Indels: 27
0.82 0.05 0.13
Matches are distributed among these distances:
56 10 0.06
57 19 0.11
59 3 0.02
60 1 0.01
61 22 0.12
62 27 0.15
63 38 0.22
64 55 0.31
65 1 0.01
ACGTcount: A:0.22, C:0.36, G:0.14, T:0.28
Consensus pattern (59 bp):
CCCTTTTAAGCCCACAACTCCGTGGCACTTTTTTCCTTCTAAGTCCACAACTCGTGGCA
Found at i:3343 original size:49 final size:49
Alignment explanation
Indices: 3290--3735 Score: 529
Period size: 43 Copynumber: 9.5 Consensus size: 49
3280 GCCCAATATC
* *
3290 GCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
* *
3339 GCTGGCCTTGACTTAGCACA-TGGCACCTTCATC-TTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
* *
3386 GTTGGCCTTG-ACCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
* *
3434 GCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATC
1 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
** *
3477 GCTGGCCTTGAATCAGCGTATTGGCATCTTCATCTTTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
* * *
3526 ACTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATC
1 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
* **
3569 GCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTTTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
* *
3618 GCTGGCCTTGAATCAGCACATT-G-A----CACCTTTAAGTCCAATATA
1 GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
* *
3661 GCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAATGTA
1 GCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTTTAAGTCCAATGTA
3713 GCTGGCCTTGAATCAGCACATTG
1 GCTGGCCTTGAATCAGCACATTG
3736 ACATCCTTTT
Statistics
Matches: 337, Mismatches: 36, Indels: 45
0.81 0.09 0.11
Matches are distributed among these distances:
43 112 0.33
44 1 0.00
45 3 0.01
46 6 0.02
47 38 0.11
48 36 0.11
49 103 0.31
52 38 0.11
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (49 bp):
GCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTA
Found at i:3532 original size:92 final size:92
Alignment explanation
Indices: 3372--3744 Score: 577
Period size: 92 Copynumber: 4.0 Consensus size: 92
3362 CACCTTCATC
* * * *
3372 TTAAGTCCAATGTAGTTGGCCTTG-ACCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGC
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGC
*
3436 TGGCCTTGAATCAGCACATTGGCACCT
66 TGGCCTTGAATCAGCACATTGACACCT
* * * *
3463 TTAAGTCCAATATCGCTGGCCTTGAATCAGCGTATTGGCATCTTCATCTTTAAGTCCAATGTAAC
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGC
*
3528 TGGCCTTGAATCAGCACATTGGCACCT
66 TGGCCTTGAATCAGCACATTGACACCT
* **
3555 TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTTTAAGTCCAATGTAGC
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGC
3620 TGGCCTTGAATCAGCACATTGACACCT
66 TGGCCTTGAATCAGCACATTGACACCT
*
3647 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAATGT
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGTCCAATGT
3712 AGCTGGCCTTGAATCAGCACATTGACATCCT
63 AGCTGGCCTTGAATCAGCACATTGACA-CCT
3743 TT
1 TT
3745 TTCTCATCTT
Statistics
Matches: 259, Mismatches: 18, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
91 21 0.08
92 189 0.73
94 2 0.01
95 42 0.16
96 5 0.02
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (92 bp):
TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGC
TGGCCTTGAATCAGCACATTGACACCT
Found at i:3723 original size:52 final size:53
Alignment explanation
Indices: 3645--3798 Score: 186
Period size: 52 Copynumber: 2.9 Consensus size: 53
3635 ACATTGACAC
3645 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
* * * *
3697 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTCTCAT
* * * * *
3752 CTTTAAG-CCTAATATCGTTGGCCGTGAATCAACATATTGGCATCTTT
1 CTTTAAGTCC-AATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT
3799 ATCACTTTTC
Statistics
Matches: 85, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
52 38 0.45
53 5 0.06
54 7 0.08
55 35 0.41
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
Found at i:4777 original size:13 final size:13
Alignment explanation
Indices: 4759--4783 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4749 ATTACTCAAA
4759 TGTATCGATACAT
1 TGTATCGATACAT
4772 TGTATCGATACA
1 TGTATCGATACA
4784 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4848 original size:52 final size:52
Alignment explanation
Indices: 4792--4920 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
4782 CACTGATCTT
*
4792 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
4844 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
4896 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
4921 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:6032 original size:23 final size:23
Alignment explanation
Indices: 5989--6034 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
5979 AAATTTAGTA
* *
5989 AATCAAGTCTAGAATCATGATTT
1 AATCAAGTCCAAAATCATGATTT
6012 AATCAAGTCCAAAATTC-TGATTT
1 AATCAAGTCCAAAA-TCATGATTT
6035 TTGAACCAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (23 bp):
AATCAAGTCCAAAATCATGATTT
Done.