Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga14g00981.M1
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: 4994
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.29
Found at i:849 original size:15 final size:15
Alignment explanation
Indices: 829--879 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
819 AAAAAACGAT
829 AACGTAAGTGACTAA
1 AACGTAAGTGACTAA
** *
844 AACGTAA-TGTTTCA
1 AACGTAAGTGACTAA
*
858 AACATAAGTGACTAA
1 AACGTAAGTGACTAA
*
873 AATGTAA
1 AACGTAA
880 TCTAAGCTAA
Statistics
Matches: 26, Mismatches: 9, Indels: 2
0.70 0.24 0.05
Matches are distributed among these distances:
14 10 0.38
15 16 0.62
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (15 bp):
AACGTAAGTGACTAA
Found at i:2665 original size:21 final size:21
Alignment explanation
Indices: 2612--2681 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
2602 CAGGACCTTC
*
2612 TAGTCCACCTTCAAGAGGAGT
1 TAGTCCACCTCCAAGAGGAGT
*
2633 TAG-CCCCACTCCAAGAGGAGT
1 TAGTCCAC-CTCCAAGAGGAGT
*
2654 TAGTCTACCTCCAAG-GGAAGT
1 TAGTCCACCTCCAAGAGG-AGT
*
2675 CAGTCCA
1 TAGTCCA
2682 ACTCAGATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
20 5 0.12
21 33 0.82
22 2 0.05
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.20
Consensus pattern (21 bp):
TAGTCCACCTCCAAGAGGAGT
Found at i:2767 original size:21 final size:21
Alignment explanation
Indices: 2737--2790 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
2727 ACTTCAGTTC
*
2737 TCAGTTCAACTTCAAGAGG-AG
1 TCAGTCCAACTTCAAG-GGTAG
*
2758 TCAGTCCAACTCCAAGGGTAG
1 TCAGTCCAACTTCAAGGGTAG
*
2779 TGAGTCCAACTT
1 TCAGTCCAACTT
2791 GGATGAGAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (21 bp):
TCAGTCCAACTTCAAGGGTAG
Found at i:2832 original size:105 final size:105
Alignment explanation
Indices: 2644--2874 Score: 309
Period size: 105 Copynumber: 2.2 Consensus size: 105
2634 AGCCCCACTC
* * * * * *
2644 CAAGAGGAGTTAGTCTACCTCCAAGGGAAGTCAGTCCAACTCAGATTAGGACATCCATCCCATCA
1 CAAGAGGAGTCAGTCCAACTCCAAGGGAAGTCAGTCCAACTCAGATGAGAACATCCAGCCCATCA
* *
2709 AGTCAATCCCAAAACTCAACTTCAGTTCTCAGTTCAACTT
66 AGTCAATCCCAAAACTCAACTTCAGTTATAAGTTCAACTT
* * ** * **
2749 CAAGAGGAGTCAGTCCAACTCCAAGGGTAGTGAGTCCAACTTGGATGAGAACATCGAGCTTATCA
1 CAAGAGGAGTCAGTCCAACTCCAAGGGAAGTCAGTCCAACTCAGATGAGAACATCCAGCCCATCA
* *
2814 AGTCAATCCCATAGCTCAACTTCAGTTATAAGTTCAACTT
66 AGTCAATCCCAAAACTCAACTTCAGTTATAAGTTCAACTT
2854 CAAGAGGAGTCAGTCCAACTC
1 CAAGAGGAGTCAGTCCAACTC
2875 GGATGAGGGC
Statistics
Matches: 109, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
105 109 1.00
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
CAAGAGGAGTCAGTCCAACTCCAAGGGAAGTCAGTCCAACTCAGATGAGAACATCCAGCCCATCA
AGTCAATCCCAAAACTCAACTTCAGTTATAAGTTCAACTT
Found at i:2932 original size:84 final size:84
Alignment explanation
Indices: 2764--2952 Score: 231
Period size: 84 Copynumber: 2.2 Consensus size: 84
2754 GGAGTCAGTC
* * * * *
2764 CAACTCCAAG-GGTAGTGAGTCCAACTTGGATGAGAACATCGAGCTTATCAAGTCAATCCCATAG
1 CAACTTCAAGAGG-AGTCAGTCCAACTCGGATGAGAACATCAACCTTATCAAGTCAATCCCATAG
*
2828 CTCAACTTCAGTTATAAGTT
65 CTCAACTCCAGTTATAAGTT
**
2848 CAACTTCAAGAGGAGTCAGTCCAACTCGGATGAGGGCATCAACCTTATCAAGTCAATCCCATAGC
1 CAACTTCAAGAGGAGTCAGTCCAACTCGGATGAGAACATCAACCTTATCAAGTCAATCCCATAGC
* *
2913 TCAGCTCCAG-TAGTTAGTT
66 TCAACTCCAGTTA-TAAGTT
*
2932 CAACTTTAAGA-GAGGTCAGTC
1 CAACTTCAAGAGGA-GTCAGTC
2953 TTACTCCAAG
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
83 4 0.04
84 85 0.93
85 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (84 bp):
CAACTTCAAGAGGAGTCAGTCCAACTCGGATGAGAACATCAACCTTATCAAGTCAATCCCATAGC
TCAACTCCAGTTATAAGTT
Found at i:3014 original size:189 final size:186
Alignment explanation
Indices: 2662--3060 Score: 455
Period size: 189 Copynumber: 2.1 Consensus size: 186
2652 GTTAGTCTAC
* *
2662 CTCCAAG-GGAAGTCAGTCCAACTCAGATTAGGACATCCATCCCATCAAGTCAATCCCAAAACTC
1 CTCCAAGAGG-AGTCAGTCCAACTCAGATGAGGACATCCAACCCATCAAGTCAATCCCAAAACTC
* * * * *
2726 AACTTCAGTTCTCAGTTCAACTTCAAGAGGAGTCAGTCCAACTCCAAGGGTAGTGAGTCCAACTT
65 AACTCCAGTACTCAGTTCAACTTCAAGAGGAGTCAGTCCAACTCCAAGGGTAATCAGTCCAACTC
* * * *
2791 GGATGAGAACATCGAGCTTATCAAGTCAATCCCATAGCTCAACTTCAGTTATAAGTTCAA
130 GAATGAGAACATCAACCTCATCAAGTCAATCCCATAGCTCAACTTCA---ATAAGTTCAA
* * * * * *
2851 CTTCAAGAGGAGTCAGTCCAACTCGGATGAGGGCAT-CAACCTTATCAAGTCAATCCCATAGCTC
1 CTCCAAGAGGAGTCAGTCCAACTCAGATGAGGACATCCAACC-CATCAAGTCAATCCCAAAACTC
* * * * **
2915 AGCTCCAGTAGTTAGTTCAACTTTAAGA-GAGGTCAGTCTTACTCCAAGGGTAATCAGTCCAACT
65 AACTCCAGTACTCAGTTCAACTTCAAGAGGA-GTCAGTCCAACTCCAAGGGTAATCAGTCCAACT
** * *
2979 CGAATGAGGAA-ATCAACCTCATTGAGTCTATCCCATAGCTCAACTTCAATTAGTTCAA
129 CGAATGA-GAACATCAACCTCATCAAGTCAATCCCATAGCTCAACTTCAATAAGTTCAA
*
3037 CTCCAAGAGGAGTCAATCCAACTC
1 CTCCAAGAGGAGTCAGTCCAACTC
3061 CAAGCGTAGT
Statistics
Matches: 177, Mismatches: 29, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
186 31 0.18
188 6 0.03
189 135 0.76
190 5 0.03
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (186 bp):
CTCCAAGAGGAGTCAGTCCAACTCAGATGAGGACATCCAACCCATCAAGTCAATCCCAAAACTCA
ACTCCAGTACTCAGTTCAACTTCAAGAGGAGTCAGTCCAACTCCAAGGGTAATCAGTCCAACTCG
AATGAGAACATCAACCTCATCAAGTCAATCCCATAGCTCAACTTCAATAAGTTCAA
Found at i:3182 original size:21 final size:21
Alignment explanation
Indices: 3133--3185 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
3123 ACTTCAGTTA
*
3133 TCAGTTCAACTCCAAGAGGAG
1 TCAGTCCAACTCCAAGAGGAG
*
3154 TCATTCCAACTCCAAG-GGTAG
1 TCAGTCCAACTCCAAGAGG-AG
*
3175 TGAGTCCAACT
1 TCAGTCCAACT
3186 GGGATGAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (21 bp):
TCAGTCCAACTCCAAGAGGAG
Found at i:3221 original size:207 final size:205
Alignment explanation
Indices: 2861--3375 Score: 538
Period size: 207 Copynumber: 2.5 Consensus size: 205
2851 CTTCAAGAGG
* * * * *
2861 AGTCAGTCCAACTCGGATGAGGGCATCAACCTTATCAAGTCAATCCCATAGCTCAGCTCCAG-TA
1 AGTCAGTCCAACTC-GATAAGGACATC-ACC-TATCAAGTCAATCCCATAGTTCAACTTCAGTTA
** **
2925 GTTAGTTCAACTTTAAGA-GAGGTCAGTCTTACTCCAAGGGTAATCAGTCCAACTCGAATGAGGA
63 -TTAGTTCAACTCCAAGAGGA-GTCAGTCCAACTCCAAGGGTAATCAGTCCAACTCGAATGAGGA
** *
2989 AATCAACCTCATTGAGTCTATCCCATAGCTCAACTTCAATT-AGTTCAACTCC-AAGAGGAGTCA
126 AATCAACCTCATCAAGTCAATCCCATAGCTCAACTTCAATTCAGTTCAAC-CCTAAGAGGAGTCA
3052 ATCCAACTCCAAGCGT
190 ATCCAACTCCAAGCGT
*
3068 AGTGAGTCCAACTCAGATAAGGACATACACCTCATCAAGTCAATCCCATAGTTCAACTTCAGTTA
1 AGTCAGTCCAACTC-GATAAGGACAT-CACCT-ATCAAGTCAATCCCATAGTTCAACTTCAGTTA
* * * * * * *
3133 TCAGTTCAACTCCAAGAGGAGTCATTCCAACTCCAAGGGTAGTGAGTCCAACTGGGATGAGGACA
63 TTAGTTCAACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAATCAGTCCAACTCGAATGAGGAAA
* * * *
3198 TCCACCTCATCAAGTCAATCCCATAGCTCAACTTCAGTTCACATTTCAACCCTAAGAGGAGTCAG
128 TCAACCTCATCAAGTCAATCCCATAGCTCAACTTCAATT--CAGTTCAACCCTAAGAGGAGTCAA
* * *
3263 TCCAATTTCAAGGGT
191 TCCAACTCCAAGCGT
* * * * * *
3278 AGTCAGTCCAATTCGAATAAGAACATCCAGCATATCGAGCCAATCCCATAGCTT-GACTTCAGTT
1 AGTCAGTCCAACTCG-ATAAGGACAT-CA-CCTATCAAGTCAATCCCATAG-TTCAACTTCAGTT
*
3342 ATTGGTTCAACTCCAA-AGGTAGTCAGTCCAACTC
62 ATTAGTTCAACTCCAAGAGG-AGTCAGTCCAACTC
3376 GGATGGGAAC
Statistics
Matches: 257, Mismatches: 39, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
206 1 0.00
207 136 0.53
208 5 0.02
209 6 0.02
210 105 0.41
211 4 0.02
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (205 bp):
AGTCAGTCCAACTCGATAAGGACATCACCTATCAAGTCAATCCCATAGTTCAACTTCAGTTATTA
GTTCAACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAATCAGTCCAACTCGAATGAGGAAATCA
ACCTCATCAAGTCAATCCCATAGCTCAACTTCAATTCAGTTCAACCCTAAGAGGAGTCAATCCAA
CTCCAAGCGT
Found at i:3421 original size:84 final size:85
Alignment explanation
Indices: 3271--3459 Score: 242
Period size: 84 Copynumber: 2.3 Consensus size: 85
3261 AGTCCAATTT
* **
3271 CAAG-GGTAGTCAGTCCAATTCGAATAAGAACATCCAGCATATCGAGCCAATCCCATAGCTTGAC
1 CAAGAGGTAGTCAGTCCAACTCGAATAAGAACATCCAGCATATCGAGCCAATCCCATAGCTCAAC
**
3335 TTCAGTTATTGGTTCAACTC
66 TTCAGTTATCAGTTCAACTC
* ** * *
3355 CAA-AGGTAGTCAGTCCAACTCGGATGGGAACATCCA-CCTCATCGAGTCAATCCCATAGCTCAA
1 CAAGAGGTAGTCAGTCCAACTCGAATAAGAACATCCAGCAT-ATCGAGCCAATCCCATAGCTCAA
3418 CTTCAGTTATCAGTTCAACTC
65 CTTCAGTTATCAGTTCAACTC
*
3439 CAAGAGG-AGTAAGTCCAACTC
1 CAAGAGGTAGTCAGTCCAACTC
3460 CAAATGTTAT
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
83 2 0.02
84 86 0.95
85 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (85 bp):
CAAGAGGTAGTCAGTCCAACTCGAATAAGAACATCCAGCATATCGAGCCAATCCCATAGCTCAAC
TTCAGTTATCAGTTCAACTC
Found at i:3471 original size:42 final size:42
Alignment explanation
Indices: 3423--3504 Score: 137
Period size: 42 Copynumber: 2.0 Consensus size: 42
3413 CTCAACTTCA
3423 GTTATCAGTTCAACTCCAAGAGGAGTAAGTCCAACTCCAAAT
1 GTTATCAGTTCAACTCCAAGAGGAGTAAGTCCAACTCCAAAT
* * *
3465 GTTATCATTTCAATTCCAAGAGGAGTCAGTCCAACTCCAA
1 GTTATCAGTTCAACTCCAAGAGGAGTAAGTCCAACTCCAA
3505 TCAGGACATC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (42 bp):
GTTATCAGTTCAACTCCAAGAGGAGTAAGTCCAACTCCAAAT
Found at i:3503 original size:21 final size:21
Alignment explanation
Indices: 3427--3504 Score: 70
Period size: 21 Copynumber: 3.7 Consensus size: 21
3417 ACTTCAGTTA
*
3427 TCAGTTCAACTCCAAGAGGAG
1 TCAGTCCAACTCCAAGAGGAG
* *
3448 TAAGTCCAACTCCAA-ATGTTA-
1 TCAGTCCAACTCCAAGA-G-GAG
* * *
3469 TCATTTCAATTCCAAGAGGAG
1 TCAGTCCAACTCCAAGAGGAG
3490 TCAGTCCAACTCCAA
1 TCAGTCCAACTCCAA
3505 TCAGGACATC
Statistics
Matches: 42, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
20 2 0.05
21 38 0.90
22 2 0.05
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (21 bp):
TCAGTCCAACTCCAAGAGGAG
Found at i:3564 original size:126 final size:126
Alignment explanation
Indices: 3347--3588 Score: 391
Period size: 126 Copynumber: 1.9 Consensus size: 126
3337 CAGTTATTGG
** *
3347 TTCAACTCCAAAGGTAGTCAGTCCAACTCGGATGGGAACATCCACCTCATCGAGTCAATCCCATA
1 TTCAACTCCAAAGGTAGTCAGTCCAACTCCAATAGGAACATCCACCTCATCGAGTCAATCCCATA
3412 GCTCAACTTCAGTTATCAGTTCAACTCCAAGAGGAG-TAAGTCCAACTCCAAATGTTATCAT
66 GCTCAACTTCAGTTATCAGTTCAACTCCAAGAGG-GTTAAGTCCAACTCCAAATGTTATCAT
*
3473 TTCAATTCCAAGAGG-AGTCAGTCCAACTCCAATCAGG-ACATCCACCTCATCGAGTCAATCCCA
1 TTCAACTCCAA-AGGTAGTCAGTCCAACTCCAAT-AGGAACATCCACCTCATCGAGTCAATCCCA
*
3536 TAGCTCAACTTCAGTTATCAGTTCAACTCCAAGAGGGTTCAGTCCAACTCCAA
64 TAGCTCAACTTCAGTTATCAGTTCAACTCCAAGAGGGTTAAGTCCAACTCCAA
3589 GGGTAGTTAG
Statistics
Matches: 108, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
125 1 0.01
126 102 0.94
127 5 0.05
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.24
Consensus pattern (126 bp):
TTCAACTCCAAAGGTAGTCAGTCCAACTCCAATAGGAACATCCACCTCATCGAGTCAATCCCATA
GCTCAACTTCAGTTATCAGTTCAACTCCAAGAGGGTTAAGTCCAACTCCAAATGTTATCAT
Found at i:3583 original size:21 final size:21
Alignment explanation
Indices: 3553--3606 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
3543 ACTTCAGTTA
*
3553 TCAGTTCAACTCCAAGAGG-GT
1 TCAGTCCAACTCCAAG-GGAGT
3574 TCAGTCCAACTCCAAGGGTAGT
1 TCAGTCCAACTCCAAGGG-AGT
3596 T-AGTCCAACTC
1 TCAGTCCAACTC
3607 GGATGAGGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 2 0.07
21 25 0.83
22 3 0.10
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (21 bp):
TCAGTCCAACTCCAAGGGAGT
Found at i:3688 original size:21 final size:21
Alignment explanation
Indices: 3659--3711 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
3649 CTTCAGTTAT
*
3659 CAGTTCAACTCCAAGAGG-AGC
1 CAGTCCAACTCCAAG-GGTAGC
*
3680 CAGTCCAACTCCAAGGGTAGT
1 CAGTCCAACTCCAAGGGTAGC
*
3701 TAGTCCAACTC
1 CAGTCCAACTC
3712 AGATGAGGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (21 bp):
CAGTCCAACTCCAAGGGTAGC
Found at i:3795 original size:105 final size:104
Alignment explanation
Indices: 2848--3777 Score: 801
Period size: 105 Copynumber: 8.9 Consensus size: 104
2838 GTTATAAGTT
* * * * *
2848 CAACTTCAAGAGG-AGTCAGTCCAACTCGGATGAGGGCATCAACCTTATCAAGTCAATCCCATAG
1 CAACTCCAAG-GGTAGTCAGTCCAACTC-GATGAGGACATCCACCTCATCGAGTCAATCCCATAG
* * * **
2912 CTCAGCTCCAG-TAGTTAGTTCAACTTTAAGA-GAGGTCAGTC
64 CTCAACTTCAGTTA-TCAGTTCAACTCCAAGAGGA-GTCAGTC
** * * * * *
2953 TTACTCCAAGGGTAATCAGTCCAACTCGAATGAGGAAATCAACCTCATTGAGTCTATCCCATAGC
1 CAACTCCAAGGGTAGTCAGTCCAACTCG-ATGAGGACATCCACCTCATCGAGTCAATCCCATAGC
* *
3018 TCAACTTCA---ATTAGTTCAACTCCAAGAGGAGTCAATC
65 TCAACTTCAGTTATCAGTTCAACTCCAAGAGGAGTCAGTC
* * * * * *
3055 CAACTCCAAGCGTAGTGAGTCCAACTCAGATAAGGACATACACCTCATCAAGTCAATCCCATAGT
1 CAACTCCAAGGGTAGTCAGTCCAACTC-GATGAGGACATCCACCTCATCGAGTCAATCCCATAGC
*
3120 TCAACTTCAGTTATCAGTTCAACTCCAAGAGGAGTCATTC
65 TCAACTTCAGTTATCAGTTCAACTCCAAGAGGAGTCAGTC
* * *
3160 CAACTCCAAGGGTAGTGAGTCCAACTGGGATGAGGACATCCACCTCATCAAGTCAATCCCATAGC
1 CAACTCCAAGGGTAGTCAGTCCAACT-CGATGAGGACATCCACCTCATCGAGTCAATCCCATAGC
*
3225 TCAACTTCAGTTCA-CATTTCAAC-CCTAAGAGGAGTCAGTC
65 TCAACTTCAGTT-ATCAGTTCAACTCC-AAGAGGAGTCAGTC
* * * * * * *
3265 CAATTTCAAGGGTAGTCAGTCCAATTCGAATAAGAACATCCAGCAT-ATCGAGCCAATCCCATAG
1 CAACTCCAAGGGTAGTCAGTCCAACTCG-ATGAGGACATCCA-CCTCATCGAGTCAATCCCATAG
** **
3329 CTTGACTTCAGTTATTGGTTCAACTCCAA-AGGTAGTCAGTC
64 CTCAACTTCAGTTATCAGTTCAACTCCAAGAGG-AGTCAGTC
* * * * * * * * * *
3370 CAACTCGGATGGG-A-ACA-TCCACCTC-ATCGA-GTCAATCC-CAT-AGCTCAACTTCAGT--T
1 CAACTC-CAAGGGTAGTCAGTCCAACTCGAT-GAGGAC-ATCCACCTCA--TCGA-GTCAATCCC
* * ** * * * * *
3426 ATCAGTTCAACTCCAAGAGGAGTAAGTCCAACTCCAA-ATGTTA-TCATTT
60 AT-AGCTCAACTTC-AG-TTA-TCAGTTCAACTCCAAGA-G-GAGTCAGTC
* * *
3475 CAATTCCAAGAGG-AGTCAGTCCAACTCCAATCAGGACATCCACCTCATCGAGTCAATCCCATAG
1 CAACTCCAAG-GGTAGTCAGTCCAACT-CGATGAGGACATCCACCTCATCGAGTCAATCCCATAG
3539 CTCAACTTCAGTTATCAGTTCAACTCCAAGAGG-GTTCAGTC
64 CTCAACTTCAGTTATCAGTTCAACTCCAAGAGGAG-TCAGTC
*
3580 CAACTCCAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCCATAGC
1 CAACTCCAAGGGTAGTCAGTCCAACTC-GATGAGGACATCCACCTCATCGAGTCAATCCCATAGC
* *
3645 TCCACTTCAGTTATCAGTTCAACTCCAAGAGGAGCCAGTC
65 TCAACTTCAGTTATCAGTTCAACTCCAAGAGGAGTCAGTC
* *
3685 CAACTCCAAGGGTAGTTAGTCCAACTCAGATGAGGACATCCATCTCATCGAGTCAATCCCATAGC
1 CAACTCCAAGGGTAGTCAGTCCAACTC-GATGAGGACATCCACCTCATCGAGTCAATCCCATAGC
*
3750 TCAACTTCAGTTA-CAAGTCCAACTCCAA
65 TCAACTTCAGTTATC-AGTTCAACTCCAA
3778 TGGTAGCTAG
Statistics
Matches: 671, Mismatches: 110, Indels: 88
0.77 0.13 0.10
Matches are distributed among these distances:
100 4 0.01
101 5 0.01
102 95 0.14
103 15 0.02
104 19 0.03
105 478 0.71
106 16 0.02
107 12 0.02
108 18 0.03
109 8 0.01
110 1 0.00
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (104 bp):
CAACTCCAAGGGTAGTCAGTCCAACTCGATGAGGACATCCACCTCATCGAGTCAATCCCATAGCT
CAACTTCAGTTATCAGTTCAACTCCAAGAGGAGTCAGTC
Found at i:3822 original size:84 final size:83
Alignment explanation
Indices: 3680--3945 Score: 406
Period size: 84 Copynumber: 3.2 Consensus size: 83
3670 CAAGAGGAGC
* * * *
3680 CAGTCCAACTCCAAGGGTAGTTAGTCCAACTCAGATGAGGACATCCATCTCATCGAGTCAATCCC
1 CAGTCCAACTCCAATGGTAGCTAGTCCAACTCAGATGAGGACGTCCACCTCATCGAGTCAATCCC
3745 ATAGCTCAACTTCAGTTA
66 ATAGCTCAACTTCAGTTA
*
3763 CAAGTCCAACTCCAATGGTAGCTAGTCCAACTCAGATGAGGACGTCCACCTCATCGAGTCAATCT
1 C-AGTCCAACTCCAATGGTAGCTAGTCCAACTCAGATGAGGACGTCCACCTCATCGAGTCAATCC
*
3828 CATAGCTCAACTTCTGTTA
65 CATAGCTCAACTTCAGTTA
* *
3847 CCAGTCCAACTCCAATGGTAGCTAGTCCAACTCAGATAAGGACGTCCACCTCATCGAATCAATCC
1 -CAGTCCAACTCCAATGGTAGCTAGTCCAACTCAGATGAGGACGTCCACCTCATCGAGTCAATCC
* *
3912 CATAGCTCGACCTCAGTTA
65 CATAGCTCAACTTCAGTTA
*
3931 TCAGTTCAACTCCAA
1 -CAGTCCAACTCCAA
3946 GAGGAGTCAG
Statistics
Matches: 167, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
83 1 0.01
84 165 0.99
85 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.24
Consensus pattern (83 bp):
CAGTCCAACTCCAATGGTAGCTAGTCCAACTCAGATGAGGACGTCCACCTCATCGAGTCAATCCC
ATAGCTCAACTTCAGTTA
Found at i:3879 original size:420 final size:420
Alignment explanation
Indices: 3072--3861 Score: 1164
Period size: 420 Copynumber: 1.9 Consensus size: 420
3062 AAGCGTAGTG
*
3072 AGTCCAACTCAGATAAGGACATACACCTCATCAAGTCAATCCCATAGTTCAACTTCAGTTATCAG
1 AGTCCAACTCAGATAAGGACATACACCTCATCAAGTCAATCCCATAGCTCAACTTCAGTTATCAG
* *
3137 TTCAACTCCAAGAGGAGTCATTCCAACTCCAAGGGTAGTGAGTCCAACTGGGATGAGGACATCCA
66 TTCAACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGTGAGTCCAACTCGGATGAGGACATCCA
* *
3202 CCTCATCAAGTCAATCCCATAGCTCAACTTCAGTTCACATTTCAACCCTAAGAGGAGTCAGTCCA
131 CCTCATCAAGTCAATCCCATAGCTCAACTTCAGTTCACAGTTCAACCCTAAGAGGAGCCAGTCCA
* * * *
3267 ATTTCAAGGGTAGTCAGTCCAATTCGAATAAGAACATCCAGCATATCGAGCCAATCCCATAGCTT
196 ACTCCAAGGGTAGTCAGTCCAACTCGAATAAGAACATCCAGCATATCGAGCCAATCCCATAGCTC
* *** * *
3332 GACTTCAGTTATTGGTTCAACTCCAAAGGTAGTCAGTCCAACTCGGATGGGAACATCCACCTCAT
261 AACTTCAGTTACAAGTCCAACTCCAAAGGTAGTCAGTCCAACTCAGATGGGAACATCCACCTCAT
* *
3397 CGAGTCAATCCCATAGCTCAACTTCAGTTATCAGTTCAACTCCAAGAGGAGTAAGTCCAACTCCA
326 CGAGTCAATCCCATAGCTCAACTTCAGTTACCAGTCCAACTCCAAGAGGAGTAAGTCCAACTCCA
3462 AATGTTATCATTTCAATTCCAAGAGGAGTC
391 AATGTTATCATTTCAATTCCAAGAGGAGTC
* * *
3492 AGTCCAACTCCA-ATCAGGACATCCACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTATCA
1 AGTCCAACT-CAGATAAGGACATACACCTCATCAAGTCAATCCCATAGCTCAACTTCAGTTATCA
*
3556 GTTCAACTCCAAGAGG-GTTCAGTCCAACTCCAAGGGTAGTTAGTCCAACTCGGATGAGGACATC
65 GTTCAACTCCAAGAGGAG-TCAGTCCAACTCCAAGGGTAGTGAGTCCAACTCGGATGAGGACATC
* *
3620 CACCTCATCGAGTCAATCCCATAGCTCCACTTCAGTT-ATCAGTTCAACTCC-AAGAGGAGCCAG
129 CACCTCATCAAGTCAATCCCATAGCTCAACTTCAGTTCA-CAGTTCAAC-CCTAAGAGGAGCCAG
* * * * *
3683 TCCAACTCCAAGGGTAGTTAGTCCAACTC-AGATGAGGACATCCATC-TCATCGAGTCAATCCCA
192 TCCAACTCCAAGGGTAGTCAGTCCAACTCGA-ATAAGAACATCCAGCAT-ATCGAGCCAATCCCA
* *
3746 TAGCTCAACTTCAGTTACAAGTCCAACTCCAATGGTAG-CTAGTCCAACTCAGATGAGG-ACGTC
255 TAGCTCAACTTCAGTTACAAGTCCAACTCCAAAGGTAGTC-AGTCCAACTCAGATG-GGAACATC
* *
3809 CACCTCATCGAGTCAATCTCATAGCTCAACTTCTGTTACCAGTCCAACTCCAA
318 CACCTCATCGAGTCAATCCCATAGCTCAACTTCAGTTACCAGTCCAACTCCAA
3862 TGGTAGCTAG
Statistics
Matches: 330, Mismatches: 32, Indels: 16
0.87 0.08 0.04
Matches are distributed among these distances:
419 5 0.02
420 319 0.97
421 6 0.02
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (420 bp):
AGTCCAACTCAGATAAGGACATACACCTCATCAAGTCAATCCCATAGCTCAACTTCAGTTATCAG
TTCAACTCCAAGAGGAGTCAGTCCAACTCCAAGGGTAGTGAGTCCAACTCGGATGAGGACATCCA
CCTCATCAAGTCAATCCCATAGCTCAACTTCAGTTCACAGTTCAACCCTAAGAGGAGCCAGTCCA
ACTCCAAGGGTAGTCAGTCCAACTCGAATAAGAACATCCAGCATATCGAGCCAATCCCATAGCTC
AACTTCAGTTACAAGTCCAACTCCAAAGGTAGTCAGTCCAACTCAGATGGGAACATCCACCTCAT
CGAGTCAATCCCATAGCTCAACTTCAGTTACCAGTCCAACTCCAAGAGGAGTAAGTCCAACTCCA
AATGTTATCATTTCAATTCCAAGAGGAGTC
Found at i:3961 original size:21 final size:21
Alignment explanation
Indices: 3931--3984 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
3921 ACCTCAGTTA
*
3931 TCAGTTCAACTCCAAGAGG-AG
1 TCAGTCCAACTCCAAG-GGTAG
3952 TCAGTCCAACTCCAAGGGTAG
1 TCAGTCCAACTCCAAGGGTAG
*
3973 TTAGTCCAACTC
1 TCAGTCCAACTC
3985 GGATGAGGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (21 bp):
TCAGTCCAACTCCAAGGGTAG
Found at i:3962 original size:105 final size:105
Alignment explanation
Indices: 3848--4041 Score: 300
Period size: 105 Copynumber: 1.8 Consensus size: 105
3838 CTTCTGTTAC
* *
3848 CAGTCCAACTCCAATGGTAGCTAGTCCAACTCAGATAAGGACGTCCACCTCATCGAATCAATCCC
1 CAGTCCAACTCCAAGGGTAGCTAGTCCAACTCAGATAAGGACATCCACCTCATCGAATCAATCCC
* *
3913 ATAGCTCGAC-CTCAGTTATCAGTTCAACTCCAAGAGGAGT
66 ATAGCTCAACTC-CAGATATCAGTTCAACTCCAAGAGGAGT
* * * *
3953 CAGTCCAACTCCAAGGGTAGTTAGTCCAACTCGGATGAGGACATCCACCTCATCGAGTCAATCCC
1 CAGTCCAACTCCAAGGGTAGCTAGTCCAACTCAGATAAGGACATCCACCTCATCGAATCAATCCC
4018 ATAGCTCAACTCCAGATATCAGTT
66 ATAGCTCAACTCCAGATATCAGTT
4042 TTATCACTGA
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
105 79 0.99
106 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22
Consensus pattern (105 bp):
CAGTCCAACTCCAAGGGTAGCTAGTCCAACTCAGATAAGGACATCCACCTCATCGAATCAATCCC
ATAGCTCAACTCCAGATATCAGTTCAACTCCAAGAGGAGT
Done.