Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2392
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: 27474
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Found at i:1985 original size:4 final size:4
Alignment explanation
Indices: 1978--2008 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
1968 CAAAACAAAC
1978 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
2009 CACCTCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:3271 original size:33 final size:33
Alignment explanation
Indices: 3227--3305 Score: 131
Period size: 33 Copynumber: 2.4 Consensus size: 33
3217 AACTTCCTAG
3227 ATGTATCGATACAAAGATCGATGTATCGATACA
1 ATGTATCGATACAAAGATCGATGTATCGATACA
* *
3260 ATGTATTGATACAAAGATCGTTGTATCGATACA
1 ATGTATCGATACAAAGATCGATGTATCGATACA
*
3293 AGGTATCGATACA
1 ATGTATCGATACA
3306 TTTCTTTGGC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (33 bp):
ATGTATCGATACAAAGATCGATGTATCGATACA
Found at i:3290 original size:20 final size:19
Alignment explanation
Indices: 3228--3293 Score: 63
Period size: 20 Copynumber: 3.7 Consensus size: 19
3218 ACTTCCTAGA
3228 TGTATCGATACAAAGATCG
1 TGTATCGATACAAAGATCG
3247 ATGTATCGATAC--A-A---
1 -TGTATCGATACAAAGATCG
*
3261 TGTATTGATACAAAGATCG
1 TGTATCGATACAAAGATCG
3280 TTGTATCGATACAA
1 -TGTATCGATACAA
3294 GGTATCGATA
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
13 10 0.27
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
20 23 0.62
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (19 bp):
TGTATCGATACAAAGATCG
Found at i:3347 original size:13 final size:13
Alignment explanation
Indices: 3329--3362 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
3319 AGCTTCATAG
*
3329 CGATACATTGTAT
1 CGATACAATGTAT
3342 CGATACAATGTAT
1 CGATACAATGTAT
3355 CGATACAA
1 CGATACAA
3363 CACTTATGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (13 bp):
CGATACAATGTAT
Found at i:12769 original size:188 final size:189
Alignment explanation
Indices: 12388--12813 Score: 590
Period size: 189 Copynumber: 2.2 Consensus size: 189
12378 GAAATTTTTG
* * * * **
12388 ATTTTTCAT-ACCCTTACGAAAAACCCATAAGAATATGAAAATATGACTCGAGTGAATAAACGAT
1 ATTTTT-ATAACCC-TACGAAAAA-CAATAGGAATATGAAAACATGACTCAAGCAAATAAACGAT
* *
12452 CACATATTTTTTTAAAATATTAATTTAGGGAAATCAAATTTTTCTAAATTTTTAAATTTAACTTC
63 CACATATTTTTTTAAAATACTAATTTAGGGAAACCAAATTTTTCTAAATTTTTAAATTTAACTTC
* * * *
12517 TAAATTTCAAACATTATGCTTCGTACTCGATGGAAAACTAGGGGATATGAAAGGAGTTAAAA
128 TAAATTTCAAACATTATGCTTCATACCCGATGGAAAACTAGAGGATACGAAAGGAGTTAAAA
* * *
12579 ATTTTTA-AACCCTCCGGAAAACAATGGGAATATGAAAACATGACTCAAGCAAATAAACGA-CTA
1 ATTTTTATAACCCTACGAAAAACAATAGGAATATGAAAACATGACTCAAGCAAATAAACGATC-A
*
12642 CATATTTTTTTAAAAATACTAATTTAGGGAAACCAAATTTTTCTAAATTTTTAAATTTAACTTTT
65 CATATTTTTTT-AAAATACTAATTTAGGGAAACCAAATTTTTCTAAATTTTTAAATTTAACTTCT
* * *
12707 AAATTTCAAACATTATGTTTCATACCCGATGGAAATC-AGAGGATACGAAAGGTGTTAAAA
129 AAATTTCAAACATTATGCTTCATACCCGATGGAAAACTAGAGGATACGAAAGGAGTTAAAA
* *
12767 ATTTTTATACCCCTACGAAAAACCATAGGAATATGAAAACATGACTC
1 ATTTTTATAACCCTACGAAAAACAATAGGAATATGAAAACATGACTC
12814 GAGTGAGCAT
Statistics
Matches: 207, Mismatches: 24, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
187 1 0.00
188 71 0.34
189 124 0.60
190 5 0.02
191 6 0.03
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (189 bp):
ATTTTTATAACCCTACGAAAAACAATAGGAATATGAAAACATGACTCAAGCAAATAAACGATCAC
ATATTTTTTTAAAATACTAATTTAGGGAAACCAAATTTTTCTAAATTTTTAAATTTAACTTCTAA
ATTTCAAACATTATGCTTCATACCCGATGGAAAACTAGAGGATACGAAAGGAGTTAAAA
Found at i:13587 original size:55 final size:56
Alignment explanation
Indices: 13538--13642 Score: 151
Period size: 54 Copynumber: 1.9 Consensus size: 56
13528 ACAAGTGTAT
*
13538 GACATAAAGAAAGAAAACATGCAATAAAGGAAAA-CAA-AAATGAAAACAAGCTCAC
1 GACATAAAGAAA-AAAACATGCAACAAAGGAAAATCAAGAAATGAAAACAAGCTCAC
* * *
13593 GGCATAAAGAAACAAACATGCAGCAAAGGAAAATCAAGAAATGAAAACAA
1 GACATAAAGAAAAAAACATGCAACAAAGGAAAATCAAGAAATGAAAACAA
13643 TAAAGGAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
54 18 0.41
55 14 0.32
56 12 0.27
ACGTcount: A:0.61, C:0.14, G:0.16, T:0.09
Consensus pattern (56 bp):
GACATAAAGAAAAAAACATGCAACAAAGGAAAATCAAGAAATGAAAACAAGCTCAC
Found at i:14167 original size:33 final size:36
Alignment explanation
Indices: 14112--14194 Score: 109
Period size: 35 Copynumber: 2.3 Consensus size: 36
14102 ACTACTTCGA
*
14112 TTCTATTTTTTTCGTTTCTGCTATTTCGA-T-TCTGTT
1 TTCT-TTTTTTTC-TTTCTGCTATTTCGATTCTCTCTT
*
14148 TTCTTTTTTTT-TTTTTGCTATTTCGATTCTCTCTT
1 TTCTTTTTTTTCTTTCTGCTATTTCGATTCTCTCTT
14183 TTCTTTTTTTTC
1 TTCTTTTTTTTC
14195 GCTGCAATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
33 14 0.33
34 1 0.02
35 23 0.55
36 4 0.10
ACGTcount: A:0.06, C:0.17, G:0.07, T:0.70
Consensus pattern (36 bp):
TTCTTTTTTTTCTTTCTGCTATTTCGATTCTCTCTT
Found at i:14412 original size:29 final size:29
Alignment explanation
Indices: 14374--14435 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
14364 TAATTTCATT
**
14374 TTGCAGCAGTTGTTTTGTTGGTGTCTTCA
1 TTGCAGCAGTTGTTTCCTTGGTGTCTTCA
**
14403 TTGCAGCAGTTGTTTCCTTTTTGTCTTCA
1 TTGCAGCAGTTGTTTCCTTGGTGTCTTCA
14432 TTGC
1 TTGC
14436 GACAGCTGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.10, C:0.18, G:0.23, T:0.50
Consensus pattern (29 bp):
TTGCAGCAGTTGTTTCCTTGGTGTCTTCA
Found at i:14445 original size:29 final size:28
Alignment explanation
Indices: 14395--14471 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 28
14385 GTTTTGTTGG
*
14395 TGTCTTCATTGCAGCAGTTGTTTCCTTTT
1 TGTCTTCATTGCA-CAGCTGTTTCCTTTT
*
14424 TGTCTTCATTGCGACAGCTGTTTCTTTTT
1 TGTCTTCATTGC-ACAGCTGTTTCCTTTT
*
14453 TTTCTTCATTGCTACAGCT
1 TGTCTTCATTGC-ACAGCT
14472 TAATTGCTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 42 0.98
30 1 0.02
ACGTcount: A:0.12, C:0.22, G:0.16, T:0.51
Consensus pattern (28 bp):
TGTCTTCATTGCACAGCTGTTTCCTTTT
Found at i:14698 original size:5 final size:5
Alignment explanation
Indices: 14683--14713 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
14673 ATGCATGAAA
*
14683 GCAAT GAAAT GCAAT GCAAT GCAAT GCAAT G
1 GCAAT GCAAT GCAAT GCAAT GCAAT GCAAT G
14714 TTTTTGACGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.19
Consensus pattern (5 bp):
GCAAT
Found at i:14698 original size:10 final size:10
Alignment explanation
Indices: 14673--14713 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
14663 TGTGAAATGC
14673 ATGC-ATGAA
1 ATGCAATGAA
14682 A-GCAATGAA
1 ATGCAATGAA
*
14691 ATGCAATGCA
1 ATGCAATGAA
*
14701 ATGCAATGCA
1 ATGCAATGAA
14711 ATG
1 ATG
14714 TTTTTGACGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 2 0.07
9 7 0.24
10 20 0.69
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.20
Consensus pattern (10 bp):
ATGCAATGAA
Found at i:14933 original size:3 final size:3
Alignment explanation
Indices: 14915--14952 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
14905 ATTAATTAAC
*
14915 TAT TAG TAT T-T TAT TAT TA- TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
14953 TTTTTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:15645 original size:43 final size:42
Alignment explanation
Indices: 15582--15780 Score: 152
Period size: 43 Copynumber: 4.6 Consensus size: 42
15572 GACACAGTTC
* * *
15582 TTTTCTCTTTATCCTTAAGGAGCAGGACACATTCCTTGTTTCCT
1 TTTTC-CTTTGTCCTCAAGGAGCAGGACACATT-CTTCTTTCCT
* * *
15626 TTTTCCTTTGTCCTCAAGGAGCAGGACCCATTTCATCTTCTTCT
1 TTTTCCTTTGTCCTCAAGGAGCAGGACACA-TTCTTCTT-TCCT
* * * * ** *
15670 TTTCCCTTTGTCTTTAAGGAGCAAGATGCATTCTTTTTTGCCT
1 TTTTCCTTTGTCCTCAAGGAGCAGGACACATTCTTCTTT-CCT
* *
15713 TTTTCCTTTGTCCTCAAGGAGCAAGAC-C-TAT-TTCATTCTCT
1 TTTTCCTTTGTCCTCAAGGAGCAGGACACAT-TCTTCTTTC-CT
* * *
15754 TTTCCCTTTGTCCTCAAAGAGTAGGAC
1 TTTTCCTTTGTCCTCAAGGAGCAGGAC
15781 GTACTCCTTT
Statistics
Matches: 125, Mismatches: 25, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
40 1 0.01
41 30 0.24
42 3 0.02
43 57 0.46
44 34 0.27
ACGTcount: A:0.18, C:0.26, G:0.15, T:0.42
Consensus pattern (42 bp):
TTTTCCTTTGTCCTCAAGGAGCAGGACACATTCTTCTTTCCT
Found at i:15725 original size:87 final size:85
Alignment explanation
Indices: 15579--15767 Score: 256
Period size: 87 Copynumber: 2.2 Consensus size: 85
15569 CAGGACACAG
* * *
15579 TTCTTTTCTCTTTATCCTTAAGGAGCAGGACACATTCCTTGTTTCCTTTTTCCTTTGTCCTCAAG
1 TTCTTTTCCCTTTGTCCTTAAGGAGCAAGACACATTCCTTGTTTCCTTTTTCCTTTGTCCTCAAG
*
15644 GAGCAGGACCCATTTCATCTTC
66 GAGCAAGACCCATTTCA--TTC
* ** *
15666 TTCTTTTCCCTTTGTCTTTAAGGAGCAAGATGCATT-CTTTTTTGCCTTTTTCCTTTGTCCTCAA
1 TTCTTTTCCCTTTGTCCTTAAGGAGCAAGACACATTCCTTGTTT-CCTTTTTCCTTTGTCCTCAA
*
15730 GGAGCAAGACCTATTTCATTC
65 GGAGCAAGACCCATTTCATTC
15751 -TCTTTTCCCTTTGTCCT
1 TTCTTTTCCCTTTGTCCT
15768 CAAAGAGTAG
Statistics
Matches: 91, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
84 16 0.18
85 3 0.03
86 6 0.07
87 66 0.73
ACGTcount: A:0.16, C:0.26, G:0.13, T:0.44
Consensus pattern (85 bp):
TTCTTTTCCCTTTGTCCTTAAGGAGCAAGACACATTCCTTGTTTCCTTTTTCCTTTGTCCTCAAG
GAGCAAGACCCATTTCATTC
Found at i:15939 original size:31 final size:31
Alignment explanation
Indices: 15871--15951 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 31
15861 GCACCCTAGT
* *
15871 CAAAGCCTGCACAAGCTAGCGACACCTGAGT
1 CAAAGCCCGCACAAGCTAGCGACACCTGAGC
* * * * *
15902 CTAAGCCCGCATAAGTTGGCGACACCTGGGC
1 CAAAGCCCGCACAAGCTAGCGACACCTGAGC
* *
15933 CAAAGCCCACACACGCTAG
1 CAAAGCCCGCACAAGCTAG
15952 TGGCACTTAG
Statistics
Matches: 37, Mismatches: 13, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.30, C:0.35, G:0.23, T:0.12
Consensus pattern (31 bp):
CAAAGCCCGCACAAGCTAGCGACACCTGAGC
Found at i:16213 original size:31 final size:31
Alignment explanation
Indices: 16166--16246 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
16156 GCCTTAGAAT
**
16166 GTCAAAGCCTGCACAAGCTCGCAGCA-CTCGA
1 GTCAAAGCCCACACAAGCTCGCAGCATCT-GA
* * *
16197 GTCTAAA-CCCACACAAGTTGGCGGCATCTGA
1 GTC-AAAGCCCACACAAGCTCGCAGCATCTGA
16228 GTCAAAGCCCACACAAGCT
1 GTCAAAGCCCACACAAGCT
16247 GATGGCACCT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
30 3 0.07
31 33 0.80
32 5 0.12
ACGTcount: A:0.31, C:0.33, G:0.21, T:0.15
Consensus pattern (31 bp):
GTCAAAGCCCACACAAGCTCGCAGCATCTGA
Found at i:16273 original size:149 final size:150
Alignment explanation
Indices: 15869--16466 Score: 559
Period size: 149 Copynumber: 4.0 Consensus size: 150
15859 TGGCACCCTA
* * * *
15869 GTCAAAGCCTGCACAAGCTAGC-GACAC-CTGAGTCTAAGCCCGCATAAGTTGGCGACACCTGGG
1 GTCAAAGCCTGCACAAGCTAGCAG-CACTCTGAGTCTAAACCCACACAAGTTGGCGACACCTGAG
* * * * * *
15932 CCAAAGCCCACACACGCT-AGTGGCACTTAGGTTTGAGTCAAGTCCAAATTAGTTGGCACCTGTC
65 TCAAAGCCCACACAAGCTGA-TGGCACCTAAGTTCGAGTCAAGTCCAAATTAGTTGGCACCTATC
* *
15996 TAAAGAGGTCAAGCCTTAAAAT
129 TAAGGAGGTCAAGCCTTAGAAT
* * * * ** * * * *
16018 GTCACAG-CTCGCACAAGTTGGCGGCA--CTGAGTCTATGCTCACACAAGTTGGTGACATCTAAG
1 GTCAAAGCCT-GCACAAGCTAGCAGCACTCTGAGTCTAAACCCACACAAGTTGGCGACACCTGAG
* * * * * * *
16080 TCAAAGCCCACATAAGCCGGTGCCACCTAAG-TCTGAGTCAAGTCCACATTAGTTGGCGCATATC
65 TCAAAGCCCACACAAGCTGATGGCACCTAAGTTC-GAGTCAAGTCCAAATTAGTTGGCACCTATC
16144 TAAGGAGGTCAAGCCTTAGAAT
129 TAAGGAGGTCAAGCCTTAGAAT
* * *
16166 GTCAAAGCCTGCACAAGCTCGCAGCACTC-GAGTCTAAACCCACACAAGTTGGCGGCATCTGAGT
1 GTCAAAGCCTGCACAAGCTAGCAGCACTCTGAGTCTAAACCCACACAAGTTGGCGACACCTGAGT
**
16230 CAAAGCCCACACAAGCTGATGGCACCTAAGTTCGAGTCAAGTCCAAATTAGTTGGCACCCGTCTA
66 CAAAGCCCACACAAGCTGATGGCACCTAAGTTCGAGTCAAGTCCAAATTAGTTGGCACCTATCTA
16295 AGGAGGTCAAGCCTTAGAAT
131 AGGAGGTCAAGCCTTAGAAT
* ** * * * * * * * *
16315 GTTAAAGCCCACACAAGCTGGTTGCACCAAAGTCTGAGTC-AAA-GCTCACAAGCTGGTGGCACC
1 GTCAAAGCCTGCACAAGC---TAGCAGC--ACTCTGAGTCTAAACCCACACAAGTTGGCGACACC
* * * * * * * * *
16378 CGAGTTAAAGCCCAAACAAGCTGGTGGCACCAAAGTCCGAGTCAAGTCCACATTAGCTAGCACCT
61 TGAGTCAAAGCCCACACAAGCTGATGGCACCTAAGTTCGAGTCAAGTCCAAATTAGTTGGCACCT
16443 ATCTAAGGAGGTCAAGCCTTAGAA
126 ATCTAAGGAGGTCAAGCCTTAGAA
16467 AACCAAAACC
Statistics
Matches: 368, Mismatches: 67, Indels: 24
0.80 0.15 0.05
Matches are distributed among these distances:
147 1 0.00
148 117 0.32
149 137 0.37
150 4 0.01
152 5 0.01
153 93 0.25
154 6 0.02
155 5 0.01
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (150 bp):
GTCAAAGCCTGCACAAGCTAGCAGCACTCTGAGTCTAAACCCACACAAGTTGGCGACACCTGAGT
CAAAGCCCACACAAGCTGATGGCACCTAAGTTCGAGTCAAGTCCAAATTAGTTGGCACCTATCTA
AGGAGGTCAAGCCTTAGAAT
Found at i:17092 original size:59 final size:59
Alignment explanation
Indices: 17019--17151 Score: 167
Period size: 59 Copynumber: 2.3 Consensus size: 59
17009 TACATGCCTA
* * * **
17019 AAATGTATCAATACAAAACTACCCTACATTTTGGAAAGGAAATGCATCAATACATAAGT
1 AAATGTATCGATACAAAACTACCCTAAATTCTAAAAAGGAAATGCATCAATACATAAGT
* * ** *
17078 GAATGTATCGATACAAAACTACCCTAAATTCTAAAAAGGAAATGTATGGATGCATAAGT
1 AAATGTATCGATACAAAACTACCCTAAATTCTAAAAAGGAAATGCATCAATACATAAGT
*
17137 AAATGCATCGATACA
1 AAATGTATCGATACA
17152 TTCACTGTTT
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (59 bp):
AAATGTATCGATACAAAACTACCCTAAATTCTAAAAAGGAAATGCATCAATACATAAGT
Found at i:20764 original size:52 final size:52
Alignment explanation
Indices: 20679--20803 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
20669 ATATGAAAAG
* *
20679 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
20731 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
20783 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
20804 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:20916 original size:13 final size:13
Alignment explanation
Indices: 20898--20922 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20888 ACAAAAAATA
20898 TGTATCGATACAT
1 TGTATCGATACAT
20911 TGTATCGATACA
1 TGTATCGATACA
20923 ACATTTTATG
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:20918 original size:32 final size:33
Alignment explanation
Indices: 20877--20942 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
20867 AGTAGCTTAA
20877 ATTGTATCGATACAA-AAAATATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
***
20909 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
20942 A
1 A
20943 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (33 bp):
ATTGTATCGATACAACAAAATATGTATCGATAC
Found at i:24722 original size:7 final size:7
Alignment explanation
Indices: 24712--24743 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
24702 TTGATTTTTT
24712 AAATAAA
1 AAATAAA
24719 AAATAAA
1 AAATAAA
*
24726 AAATAAT
1 AAATAAA
24733 AAATAAA
1 AAATAAA
24740 AAAT
1 AAAT
24744 TAATAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (7 bp):
AAATAAA
Found at i:24747 original size:15 final size:14
Alignment explanation
Indices: 24712--24750 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
24702 TTGATTTTTT
*
24712 AAATAAAAAATAAA
1 AAATAATAAATAAA
24726 AAATAATAAATAAA
1 AAATAATAAATAAA
24740 AAATTAATAAA
1 AAA-TAATAAA
24751 AAATCAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAATAAATAAA
Found at i:25367 original size:64 final size:64
Alignment explanation
Indices: 25262--25390 Score: 204
Period size: 64 Copynumber: 2.0 Consensus size: 64
25252 AGCTTCCATT
* *
25262 AACGACAACATCCACCAACAGCAGCAGCATCTTCCAACCCACAAACTCCGGTAGTAGCTCTAGC
1 AACGACAACATCCACCAACAGCAGCAGCATCTTCCAACCCACAAACACCGGTAGTAGCTCCAGC
* * * *
25326 AACGACAGCATCCACCAATAGCAGCAGCATCTTCCAGCCCACAAACACTGGTAGTAGCTCCAGC
1 AACGACAACATCCACCAACAGCAGCAGCATCTTCCAACCCACAAACACCGGTAGTAGCTCCAGC
25390 A
1 A
25391 GCTTCTAGTA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.34, C:0.36, G:0.16, T:0.14
Consensus pattern (64 bp):
AACGACAACATCCACCAACAGCAGCAGCATCTTCCAACCCACAAACACCGGTAGTAGCTCCAGC
Found at i:25441 original size:74 final size:74
Alignment explanation
Indices: 25320--25517 Score: 200
Period size: 74 Copynumber: 2.7 Consensus size: 74
25310 CGGTAGTAGC
* * * * * * *
25320 TCTAGCAACGACAGCATCCACCAATAGCAGCAGCATCTTCCAGCCCACAAACACTGGTAGTAGCT
1 TCTAGTAACGACAACATCCACCAATAACAGCAGCAGCTTCCAGCCCACAAACACCGGCAGCAGCT
*
25385 CCAGCAGCT
66 CCAGCAACT
* * *
25394 TCTAGTAATGACAACATCCACCAATAATAGCAGCAGCTTCCAGCCCACGAACACCGGCAGCAGCT
1 TCTAGTAACGACAACATCCACCAATAACAGCAGCAGCTTCCAGCCCACAAACACCGGCAGCAGCT
*
25459 TCAGCAACT
66 CCAGCAACT
* * * * * ** *
25468 TCCAGTAGCGAGAGCATCCACCAA-AAGAAATAGTAGCTTCCAGCCCACAA
1 TCTAGTAACGACAACATCCACCAATAA-CAGCAGCAGCTTCCAGCCCACAA
25518 GCACTTCAGT
Statistics
Matches: 101, Mismatches: 22, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
73 2 0.02
74 99 0.98
ACGTcount: A:0.34, C:0.33, G:0.17, T:0.16
Consensus pattern (74 bp):
TCTAGTAACGACAACATCCACCAATAACAGCAGCAGCTTCCAGCCCACAAACACCGGCAGCAGCT
CCAGCAACT
Done.