Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2350
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: 12520
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.33
Found at i:162 original size:19 final size:19
Alignment explanation
Indices: 138--246 Score: 159
Period size: 19 Copynumber: 5.8 Consensus size: 19
128 AATCTTCAGG
138 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
157 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
176 AATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
195 GATAT--AATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
212 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
231 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
247 AGATATGATT
Statistics
Matches: 82, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
17 17 0.21
19 65 0.79
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:252 original size:36 final size:38
Alignment explanation
Indices: 145--246 Score: 181
Period size: 36 Copynumber: 2.7 Consensus size: 38
135 AGGGATATGC
*
145 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATGATATAT
183 AATCTTAGATATGATAT--AATCTTAGATATGATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATGATATAT
219 AATCTTAGATATGATATGCAATCTTAGA
1 AATCTTAGATATGATATGCAATCTTAGA
247 AGATATGATT
Statistics
Matches: 61, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
36 35 0.57
38 26 0.43
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (38 bp):
AATCTTAGATATGATATGCAATCTTAGATATGATATAT
Found at i:272 original size:22 final size:21
Alignment explanation
Indices: 138--272 Score: 105
Period size: 19 Copynumber: 6.9 Consensus size: 21
128 AATCTTCAGG
*
138 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
157 GATATGCAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
* *
176 AATATATAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
195 GATA--TAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
212 GATATATAATCTT--AGATAT
1 GATATGTAATCTTAGAGATAT
*
231 GATATGCAATCTTAGAAGATAT
1 GATATGTAATCTTAG-AGATAT
*
253 GATTTTGTAATCTTAGAGAT
1 GA-TATGTAATCTTAGAGAT
273 TTAATTTGTA
Statistics
Matches: 102, Mismatches: 8, Indels: 9
0.86 0.07 0.08
Matches are distributed among these distances:
17 17 0.17
19 62 0.61
22 12 0.12
23 11 0.11
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.39
Consensus pattern (21 bp):
GATATGTAATCTTAGAGATAT
Found at i:3153 original size:24 final size:24
Alignment explanation
Indices: 3124--3169 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3114 TAGAACAATC
* *
3124 CAAAAGGAAATGCAGGAGCAGCTT
1 CAAAAGCAAATGAAGGAGCAGCTT
*
3148 CAAAAGCAAATGAATGAGCAGC
1 CAAAAGCAAATGAAGGAGCAGC
3170 AAAAAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (24 bp):
CAAAAGCAAATGAAGGAGCAGCTT
Found at i:7366 original size:131 final size:131
Alignment explanation
Indices: 7090--10137 Score: 5389
Period size: 131 Copynumber: 23.4 Consensus size: 131
7080 TTGACAACGA
* *
7090 AGCAGATCGAAGATGGCAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATT
1 AGCAGATCGAAGATGGCGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATT
7155 CTACTT-CCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
66 CTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
7219 G
131 G
7220 AGCAGATCGAAGATGGCGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATT
1 AGCAGATCGAAGATGGCGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATT
* * *
7285 CTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAACTGTAGTG
66 CTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
7350 G
131 G
* * *
7351 AGCAGATCGAAGATGGTGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTAAAGCCAGTAAT
1 AGCAGATCGAAGATGG-CGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
* *
7416 TCTACTTTCCTGAACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
65 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
7481 GG
130 GG
7483 AGCAGATCGAAGATGGCGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATT
1 AGCAGATCGAAGATGGCGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATT
* *
7548 CTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGGTCTTAGCTCCCTAAGCAGTAGTG
66 CTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
7613 G
131 G
7614 AGCAGATCGAAGATGG-GATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATT
1 AGCAGATCGAAGATGGCGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATT
7678 CTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
66 CTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
7743 G
131 G
*
7744 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGC-GATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
7809 TCTACTTCCCT-GACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
65 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
7873 GG
130 GG
7875 AGCAGATCGAAGATGGCGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATT
1 AGCAGATCGAAGATGGCGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATT
7940 CTACTTCCCT-GACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
66 CTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
8004 G
131 G
* *
8005 AGCAGATCGAAGATGGTGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGG-CGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
8070 TCTACTTCCCTGG-CAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
65 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
8134 GG
130 GG
8136 AGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGC-GATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
8201 TCTACTT-CCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
65 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
8265 GG
130 GG
8267 AGCAGATCGAAGATGG-GATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATT
1 AGCAGATCGAAGATGGCGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATT
8331 CTACTT-CCT-GACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
66 CTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
8394 G
131 G
*
8395 AGCAGATCGAAGATGGTGGATTTTACCT-CCTGTGGTTATAGTGGAGTACATTGAAG-CAGTAAT
1 AGCAGATCGAAGATGG-CGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
8458 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
65 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
8523 GG
130 GG
8525 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGC-GATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
8590 TCTACTTCCCTGGACAA-AGTGGAATAGATTGAA-ATTTCAGATCTTATCTCCCTAAGCAGTAGT
65 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
8653 GG
130 GG
*
8655 AGCAGATCGAA-ATGGTGGATTTTACCTCCCTGTGG-TATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGG-CGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
*
8718 TCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
65 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
8783 GG
130 GG
*
8785 AGCAGATCGAAGATGGGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATT
1 AGCAGATCGAAGATGGCGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATT
*
8850 CTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
66 CTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
8915 G
131 G
8916 AGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGC-GATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
8981 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAG-TCTTATCTCCCTAAGCAGTAGT
65 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
9045 GG
130 GG
* *
9047 AACAGATCGAAGATGGTGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAG-CAGTAAT
1 AGCAGATCGAAGATGG-CGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
9111 TCTACTTCCCTGG-CAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
65 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
9175 GG
130 GG
9177 AGCAGATCGAAGATGGCGGATTTTACCT-CCTGTGGTTATAGTGGAGTACATTGAAAGCCAGTAA
1 AGCAGATCGAAGATGGC-GATTTTACCTCCCTGTGGTTATAGTGGAGTACATTG-AAGCCAGTAA
9241 TTCTACTTCCCTGGAACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTA
64 TTCTACTTCCCTGG-ACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTA
9306 GTGG
128 GTGG
*
9310 AG-AGATCGAAGATGGCGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCTAGTAATT
1 AGCAGATCGAAGATGGCGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATT
9374 CTACTT-CCT-GACAACAGTGGAATAGATTGAAGATTT-AGATCTTATCTCCCTAAGCAGTAGTG
66 CTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
9436 G
131 G
* *
9437 AGCAGATCGAA-ATGGTGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGG-CGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
*
9501 TCTACTTCCCTGGACAACA-TGGAATAGATTGAAGATTTCAGAGCTTATCTCCCTAAGCAGTAGT
65 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
*
9565 GA
130 GG
9567 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGC-GATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
9632 TCTACTT-CCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
65 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
9696 GG
130 GG
*
9698 AGCAGATCGAAGATAGG-GATTTTACCTCCCTGTGGTTATAGTGGAGTATATTGAAGCCAGTAAT
1 AGCAGATCGAAGAT-GGCGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
9762 TCTACTTCCCTGGACAACA-TGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
65 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
9826 GG
130 GG
*
9828 AGCAGATGGAAGATGGCGGATTTTACCT-CCTGTGGTTATAGTGGAGT-CATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGC-GATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
9891 TCTACTTCCCTGG---ACAGTGGAATAGATTGAAGATTTCAGATC-TATCTCCCTAAGCAGTAGT
65 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
9952 GG
130 GG
*
9954 AGCAGATCGAA-ATGGGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATT
1 AGCAGATCGAAGATGGCGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATT
*
10018 CTACTTCACTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
66 CTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
10083 G
131 G
*
10084 AGCAGATCGAAGATGGTAGATTTTA-C-CCCTGTGGTTA-AGTGGAGTACATTGAAG
1 AGCAGATCGAAGATGG-CGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAG
10138 AGTACATTGA
Statistics
Matches: 2814, Mismatches: 54, Indels: 101
0.95 0.02 0.03
Matches are distributed among these distances:
124 10 0.00
125 23 0.01
126 62 0.02
127 58 0.02
128 215 0.08
129 278 0.10
130 830 0.29
131 942 0.33
132 341 0.12
133 55 0.02
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.29
Consensus pattern (131 bp):
AGCAGATCGAAGATGGCGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATT
CTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
G
Found at i:7826 original size:261 final size:262
Alignment explanation
Indices: 7090--10137 Score: 5403
Period size: 261 Copynumber: 11.7 Consensus size: 262
7080 TTGACAACGA
** *
7090 AGCAGATCGAAGATGGCAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATT
1 AGCAGATCGAAGATGGGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATT
7155 CTACTT-CCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
66 CTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
7219 GAGCAGATCGAAGATGGC-GATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAA
131 GAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAA
* * *
7283 TTCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAACTGTAG
196 TTCTACTTCCCT-GACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAG
7348 TGG
260 TGG
* *
7351 AGCAGATCGAAGATGGTGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTAAAGCCAGTAAT
1 AGCAGATCGAAGATGG-GGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
* *
7416 TCTACTTTCCTGAACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
65 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
7481 GGAGCAGATCGAAGATGGC-GATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTA
130 GGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTA
* *
7545 ATTCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGGTCTTAGCTCCCTAAGCAGTA
195 ATTCTACTTCCCT-GACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTA
7610 GTGG
259 GTGG
7614 AGCAGATCGAAGAT-GGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATT
1 AGCAGATCGAAGATGGGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATT
7678 CTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
66 CTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
*
7743 GAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA
131 GAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAA
7808 TTCTACTTCCCTGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
196 TTCTACTTCCCTGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
7873 GG
261 GG
*
7875 AGCAGATCGAAGATGGCGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATT
1 AGCAGATCGAAGATGGGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATT
7940 CTACTTCCCT-GACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
66 CTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
* *
8004 GAGCAGATCGAAGATGGTGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA
131 GAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAA
*
8069 TTCTACTTCCCTGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
196 TTCTACTTCCCTGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
8134 GG
261 GG
*
8136 AGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGG-GGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
8201 TCTACTT-CCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
65 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
8265 GGAGCAGATCGAAGAT-G-GGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTA
130 GGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTA
8328 ATTCTACTT-CCTGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAG
195 ATTCTACTTCCCTGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAG
8392 TGG
260 TGG
8395 AGCAGATCGAAGATGGTGGATTTTACCT-CCTGTGGTTATAGTGGAGTACATTGAAG-CAGTAAT
1 AGCAGATCGAAGATGG-GGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
8458 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
65 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
8523 GGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTA
130 GGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTA
8588 ATTCTACTTCCCTGGACAA-AGTGGAATAGATTGAA-ATTTCAGATCTTATCTCCCTAAGCAGTA
195 ATTCTACTTCCCT-GACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTA
8651 GTGG
259 GTGG
8655 AGCAGATCGAA-ATGGTGGATTTTACCTCCCTGTGG-TATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGG-GGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
*
8718 TCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
65 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
8783 GGAGCAGATCGAAGATGG-GGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTA
130 GGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTA
*
8847 ATTCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTA
195 ATTCTACTTCCCT-GACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTA
8912 GTGG
259 GTGG
*
8916 AGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGG-GGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
8981 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAG-TCTTATCTCCCTAAGCAGTAGT
65 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
* *
9045 GGAACAGATCGAAGATGGTGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAG-CAGTA
130 GGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTA
*
9109 ATTCTACTTCCCTGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAG
195 ATTCTACTTCCCTGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAG
9174 TGG
260 TGG
9177 AGCAGATCGAAGATGGCGGATTTTACCT-CCTGTGGTTATAGTGGAGTACATTGAAAGCCAGTAA
1 AGCAGATCGAAGATGG-GGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTG-AAGCCAGTAA
9241 TTCTACTTCCCTGGAACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTA
64 TTCTACTTCCCTGG-ACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTA
*
9306 GTGGAG-AGATCGAAGATGGC-GATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCTAG
128 GTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAG
9369 TAATTCTACTT-CCTGACAACAGTGGAATAGATTGAAGATTT-AGATCTTATCTCCCTAAGCAGT
193 TAATTCTACTTCCCTGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
9432 AGTGG
258 AGTGG
*
9437 AGCAGATCGAA-ATGGTGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGG-GGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAAT
*
9501 TCTACTTCCCTGGACAACA-TGGAATAGATTGAAGATTTCAGAGCTTATCTCCCTAAGCAGTAGT
65 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
*
9565 GAAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTA
130 GGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTA
9630 ATTCTACTT-CCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTA
195 ATTCTACTTCCCT-GACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTA
9694 GTGG
259 GTGG
* *
9698 AGCAGATCGAAGATAGGGATTTTACCTCCCTGTGGTTATAGTGGAGTATATTGAAGCCAGTAATT
1 AGCAGATCGAAGATGGGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATT
9763 CTACTTCCCTGGACAACA-TGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
66 CTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
*
9827 GAGCAGATGGAAGATGGCGGATTTTACCT-CCTGTGGTTATAGTGGAGT-CATTGAAGCCAGTAA
131 GAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAA
*
9890 TTCTACTTCCCTG--GACAGTGGAATAGATTGAAGATTTCAGATC-TATCTCCCTAAGCAGTAGT
196 TTCTACTTCCCTGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
9952 GG
261 GG
9954 AGCAGATCGAA-ATGGGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATT
1 AGCAGATCGAAGATGGGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATT
*
10018 CTACTTCACTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
66 CTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
**
10083 GAGCAGATCGAAGATGGTAGATTTTA-C-CCCTGTGGTTA-AGTGGAGTACATTGAAG
131 GAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAG
10138 AGTACATTGA
Statistics
Matches: 2702, Mismatches: 53, Indels: 70
0.96 0.02 0.02
Matches are distributed among these distances:
254 8 0.00
255 87 0.03
256 101 0.04
257 90 0.03
258 121 0.04
259 303 0.11
260 400 0.15
261 826 0.31
262 434 0.16
263 332 0.12
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.29
Consensus pattern (262 bp):
AGCAGATCGAAGATGGGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATT
CTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTG
GAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAA
TTCTACTTCCCTGACAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
GG
Found at i:9164 original size:43 final size:43
Alignment explanation
Indices: 7434--9424 Score: 312
Period size: 44 Copynumber: 45.9 Consensus size: 43
7424 CCTGAACAAC
* * *
7434 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCCT-GGCAAT
** * * * * **
7478 AGTGGAGCAGATCGAAGATGGC-GATTTTACCTCCCTGTGGTTAT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCC--TGGCAAT
* * *
7522 AGTGGAGTACATTGAAGCCA-GT-A-AT-TCTA-CTTCCCTGGACAAC
1 AGTGGAATAGATTGAAG--ATGTCAGATCT-TATC-TCCCTGG-CAAT
* * * * *
7565 AGTGGAATAGATTGAAGATTTCAGGTCTTAGCTCCCTAAGCAGT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCCT-GGCAAT
** * * * * **
7609 AGTGGAGCAGATCGAAGATG--GGATTTTACCTCCCTGTGGTTAT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCC--TGGCAAT
* * *
7652 AGTGGAGTACATTGAAGCCA-GT-A-AT-TCTA-CTTCCCTGGACAAC
1 AGTGGAATAGATTGAAG--ATGTCAGATCT-TATC-TCCCTGG-CAAT
* * *
7695 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCCT-GGCAAT
** * * * * * ** *
7739 AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTAC
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCC--TGGCAAT
* * * *
7784 AGTGGAGTACATTGAAGCCA-GT-A-AT-TCTA-CTTCCCTGACAAC
1 AGTGGAATAGATTGAAG--ATGTCAGATCT-TATC-TCCCTGGCAAT
* * *
7826 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCCT-GGCAAT
** * * * * **
7870 AGTGGAGCAGATCGAAGATGGC-GATTTTACCTCCCTGTGGTTAT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCC--TGGCAAT
* * * *
7914 AGTGGAGTACATTGAAGCCA-GT-A-AT-TCTA-CTTCCCTGACAAC
1 AGTGGAATAGATTGAAG--ATGTCAGATCT-TATC-TCCCTGGCAAT
* * *
7956 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCCT-GGCAAT
** * * * * ** *
8000 AGTGGAGCAGATCGAAGATGGT-GGATTTTACCTCCCTGTGGTTAC
1 AGTGGAATAGATTGAAGAT-GTCAGATCTTATCTCCC--TGGCAAT
* * *
8045 AGTGGAGTACATTGAAGCCA-GT-A-AT-TCTA-CTTCCCTGGCAAC
1 AGTGGAATAGATTGAAG--ATGTCAGATCT-TATC-TCCCTGGCAAT
* * *
8087 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCCT-GGCAAT
** * * * * **
8131 AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTAT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCC--TGGCAAT
* * * *
8176 AGTGGAGTACATTGAAGCCA-GT-A-AT-TCTA-CTTCCTGGACAAC
1 AGTGGAATAGATTGAAG--ATGTCAGATCT-TATCTCCCTGG-CAAT
* * *
8218 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCCT-GGCAAT
** * * * * **
8262 AGTGGAGCAGATCGAAGATG--GGATTTTACCTCCCTGTGGTTAT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCC--TGGCAAT
* * * * *
8305 AGTGGAGTACATTGAAGCCA-GT-A-AT-TCTA-CTTCCTGACAAC
1 AGTGGAATAGATTGAAG--ATGTCAGATCT-TATCTCCCTGGCAAT
* * *
8346 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCCT-GGCAAT
** * * * * * **
8390 AGTGGAGCAGATCGAAGATGGT-GGATTTTACCTCCTGTGGTTAT
1 AGTGGAATAGATTGAAGAT-GTCAGATCTTATCTCC-CTGGCAAT
* * *
8434 AGTGGAGTACATTGAAGCA-GT-A-AT-TCTA-CTTCCCTGGACAAC
1 AGTGGAATAGATTGAAG-ATGTCAGATCT-TATC-TCCCTGG-CAAT
* * *
8476 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCCT-GGCAAT
** * * * * * **
8520 AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTAT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCC--TGGCAAT
* *
8565 AGTGGAGTACATTGAAGCCA-GT-A-AT-TCTA-CTTCCCTGGACAA-
1 AGTGGAATAGATTGAAG--ATGTCAGATCT-TATC-TCCCTGG-CAAT
* * *
8607 AGTGGAATAGATTGAA-ATTTCAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCCT-GGCAAT
** * * * * **
8650 AGTGGAGCAGATCGAA-ATGGT-GGATTTTACCTCCCTGTGGTAT
1 AGTGGAATAGATTGAAGAT-GTCAGATCTTATCTCCCTG-GCAAT
* * *
8693 AGTGGAGTACATTGAAGCCA-GT-A-AT-TCTA-CTTCCCTGGGCAAC
1 AGTGGAATAGATTGAAG--ATGTCAGATCT-TATC-TCCCT-GGCAAT
* * *
8736 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCCT-GGCAAT
** * ** * * **
8780 AGTGGAGCAGATCGAAGATG-GGGATTTTACCTCCCTGTGGTTAT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCC--TGGCAAT
* * *
8824 AGTGGAGTACATTGAAGCCA-GT-A-AT-TCTA-CTTCCCTGGGCAAC
1 AGTGGAATAGATTGAAG--ATGTCAGATCT-TATC-TCCCT-GGCAAT
* * *
8867 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCCT-GGCAAT
** * * * * **
8911 AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTAT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCC--TGGCAAT
* * *
8956 AGTGGAGTACATTGAAGCCA-GT-A-AT-TCTA-CTTCCCTGGACAAC
1 AGTGGAATAGATTGAAG--ATGTCAGATCT-TATC-TCCCTGG-CAAT
* * *
8999 AGTGGAATAGATTGAAGATTTCAG-TCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCCT-GGCAAT
* * * * * **
9042 AGTGGAACAGATCGAAGATGGT-GGATTTTACCTCCCTGTGGTTAT
1 AGTGGAATAGATTGAAGAT-GTCAGATCTTATCTCCC--TGGCAAT
* * *
9087 AGTGGAGTACATTGAAGCA-GT-A-AT-TCTA-CTTCCCTGGCAAC
1 AGTGGAATAGATTGAAG-ATGTCAGATCT-TATC-TCCCTGGCAAT
* * *
9128 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCCT-GGCAAT
** * * * * * * **
9172 AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCTGTGGTTAT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCC-CTGGCAAT
* * * *
9216 AGTGGAGTACATTGAA-A-GCCAGTAAT-TCTA-CTTCCCTGGAACAAC
1 AGTGGAATAGATTGAAGATGTCAG--ATCT-TATC-TCCCTGG--CAAT
* * *
9261 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCCT-GGCAAT
* * * * * **
9305 AGTGG-AGAGATCGAAGATGGC-GATTTTACCTCCCTGTGGTTAT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCC--TGGCAAT
* * * * * *
9348 AGTGGAGTACATTGAAGCTAGT-A-AT-TCTA-CTTCCTGACAAC
1 AGTGGAATAGATTGAAGAT-GTCAGATCT-TATCTCCCTGGCAAT
*
9389 AGTGGAATAGATTGAAGAT-TTAGATCTTATCTCCCT
1 AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCCT
9425 AAGCAGTAGT
Statistics
Matches: 1372, Mismatches: 385, Indels: 382
0.64 0.18 0.18
Matches are distributed among these distances:
39 3 0.00
40 8 0.01
41 81 0.06
42 194 0.14
43 349 0.25
44 561 0.41
45 149 0.11
46 19 0.01
47 8 0.01
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.29
Consensus pattern (43 bp):
AGTGGAATAGATTGAAGATGTCAGATCTTATCTCCCTGGCAAT
Found at i:10142 original size:12 final size:12
Alignment explanation
Indices: 10125--10149 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10115 TGGTTAAGTG
10125 GAGTACATTGAA
1 GAGTACATTGAA
10137 GAGTACATTGAA
1 GAGTACATTGAA
10149 G
1 G
10150 CCAGTAATCA
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:0.40, C:0.08, G:0.28, T:0.24
Consensus pattern (12 bp):
GAGTACATTGAA
Found at i:10579 original size:22 final size:22
Alignment explanation
Indices: 10519--10576 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
10509 AATCTTCAGG
10519 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
10538 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
10560 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
10577 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Done.