Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011921.1 Corchorus olitorius cultivar O-4 contig11954, whole genome shotgun sequence
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: 12006
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.36
Found at i:384 original size:154 final size:154
Alignment explanation
Indices: 1--1036 Score: 1557
Period size: 154 Copynumber: 6.8 Consensus size: 154
* * * *
1 CCGTTTTGAATCGTCTTCGGTTTGGCAACCCTCAATGCTTTTCTATCCAATGTTTATGGCCTAAC
1 CCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAAC
* * * *
66 TATAATCATATTGGTGAGATTAGTCAACTTTGATGTTTTTAGCTCATTTGGAACACTTG-TA-TT
66 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
* **
129 TGGGCATATCTAGGCCCATTAGT-
131 TGGGCCTATCGGGGCCCATTAGTG
* * *
152 CCGTTTTTAATCGTCTTCGATTTAGCAACCCTCAATGC-TTTCTTTCCATTGTTTATGGCCTAAC
1 CCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAAC
*
216 TATAATCATTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
66 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
* *
281 TTGGCCTATCGGGGCCCATTAGTT
131 TGGGCCTATCGGGGCCCATTAGTG
* *
305 CCGTTTAGAATCGTCTTCGATTTGGCAAACCGCAATGCTTTTCTTTCCATTGTTTATGGCCTAAC
1 CCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAAC
370 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
66 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
*
435 TGGGCCTATCGGGGCCCATTAGTT
131 TGGGCCTATCGGGGCCCATTAGTG
* * *
459 CCCTTTTGAATCGTCTTCGATATGGCAAACCACAATGCTTTTCTTTCCATTGTTTATGGCCTAAC
1 CCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAAC
* * *
524 TATAATCCTTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAGCTCATTTGGAACACTTGTT-GTT
66 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
* *
588 TGGGCCTATTGGGGACCATTAGTG
131 TGGGCCTATCGGGGCCCATTAGTG
* *
612 ACGTTTTGAATCCTCTTCGATTTGGCAAACCAT-AATGCTTTTCTTTCCATTGTTTATGGCCTAA
1 CCGTTTTGAATCGTCTTCGATTTGGCAAACC-TCAATGCTTTTCTTTCCATTGTTTATGGCCTAA
* *
676 CTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACATGTTATT
65 CTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATT
* * *
741 TTGGGCATTTCGGGGCCCATAAGTG
130 TTGGGCCTATCGGGGCCCATTAGTG
* *
766 ACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTT-TTTCCATTCTTTATGGCCTAAC
1 CCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAAC
* * * * *
830 TATAATCATTCTGGTGAGATTAGTCAACTGTGACGTTTTTAGCTCATTTGGAACTCTTGATATTT
66 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
*
895 TGGGCCTATTGGGGCCCATTAGTG
131 TGGGCCTATCGGGGCCCATTAGTG
* * *
919 ACGTTTTGAATCCTCTTCGATTTGGAAAACCTCAATGCTTTTCTTTCCATTGTTTAT-GCCGTAA
1 CCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCC-TAA
* * *
983 CTATGATCCTTTTGGTAAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
65 CTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
1037 TAGTGACGTT
Statistics
Matches: 810, Mismatches: 66, Indels: 15
0.91 0.07 0.02
Matches are distributed among these distances:
150 78 0.10
151 37 0.05
152 21 0.03
153 317 0.39
154 357 0.44
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (154 bp):
CCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAAC
TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
TGGGCCTATCGGGGCCCATTAGTG
Found at i:675 original size:307 final size:306
Alignment explanation
Indices: 2--1036 Score: 1571
Period size: 307 Copynumber: 3.4 Consensus size: 306
1 C
* * * * *
2 CGTTTTGAATCGTCTTCGGTTTGGCAACCCTCAATGCTTTTCTATCCAATGTTTATGGCCTAACT
1 CGTTTTGAATCCTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACT
* * * *
67 ATAATCATATTGGTGAGATTAGTCAACTTTGATGTTTTTAGCTCATTTGGAACACTTG-TA-TTT
66 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT
** * * *
130 GGGCATATCTAGGCCCATTAG-TCCGTTTTTAATCGTCTTCGATTTAGCAACCCTCAATGC-TTT
131 GGGCATATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTT
193 CTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAG
196 CTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAG
* * **
258 CTCATTTGGAACACTTGTTATTTTTGGCCTATCGGGGCCCATTAGTTC
261 CTCATTTGGAACACTTG-T-TTTTGGGCCTATTGGGGCCCATTAGTGA
* * *
306 CGTTTAGAATCGTCTTCGATTTGGCAAACCGCAATGCTTTTCTTTCCATTGTTTATGGCCTAACT
1 CGTTTTGAATCCTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACT
371 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT
66 ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT
* * * *
436 GGGCCTATCGGGGCCCATTAGTTCCCTTTTGAATCGTCTTCGATATGGCAAACCACAATGCTTTT
131 GGGCATATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTT
*
501 CTTTCCATTGTTTATGGCCTAACTATAATCCTTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAG
196 CTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAG
*
566 CTCATTTGGAACACTTGTTGTTTGGGCCTATTGGGGACCATTAGTGA
261 CTCATTTGGAACACTTGTT-TTTGGGCCTATTGGGGCCCATTAGTGA
613 CGTTTTGAATCCTCTTCGATTTGGCAAACCAT-AATGCTTTTCTTTCCATTGTTTATGGCCTAAC
1 CGTTTTGAATCCTCTTCGATTTGGCAAACC-TCAATGCTTTTCTTTCCATTGTTTATGGCCTAAC
* *
677 TATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACATGTTATTT
65 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTT
* * **
742 TGGGCATTTCGGGGCCCATAAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTT
130 TGGGCATATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTT
* * * * *
807 T-TTTCCATTCTTTATGGCCTAACTATAATCATTCTGGTGAGATTAGTCAACTGTGACGTTTTTA
195 TCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGGGAAGTTTTTA
*
871 GCTCATTTGGAACTCTTGATATTTTGGGCCTATTGGGGCCCATTAGTGA
260 GCTCATTTGGAACACTTG-T-TTTTGGGCCTATTGGGGCCCATTAGTGA
*
920 CGTTTTGAATCCTCTTCGATTTGGAAAACCTCAATGCTTTTCTTTCCATTGTTTAT-GCCGTAAC
1 CGTTTTGAATCCTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCC-TAAC
* * *
984 TATGATCCTTTTGGTAAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
65 TATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
1037 TAGTGACGTT
Statistics
Matches: 672, Mismatches: 49, Indels: 17
0.91 0.07 0.02
Matches are distributed among these distances:
304 113 0.17
305 2 0.00
306 100 0.15
307 372 0.55
308 85 0.13
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (306 bp):
CGTTTTGAATCCTCTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTTATGGCCTAACT
ATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGTTATTTT
GGGCATATCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTT
CTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAG
CTCATTTGGAACACTTGTTTTTGGGCCTATTGGGGCCCATTAGTGA
Found at i:1133 original size:123 final size:123
Alignment explanation
Indices: 914--1153 Score: 383
Period size: 123 Copynumber: 2.0 Consensus size: 123
904 TGGGGCCCAT
914 TAGTGACGTTTTGAATCCTCTTCGATTTGGAAAACCTCAATGCTTTTCTTTCCATTGTTTATGCC
1 TAGTGACGTTTTGAATCCTCTTCGATTTGGAAAACCTCAATGCTTTTCTTTCCATTGTTTATGCC
* ** *
979 GTAACTATGATCCTTTTGGTAAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
66 GTAACTATAATAATTTTGGTAAGATTAGTCCACTGTAAAGTTTTTAGCTCATTTGGAA
* * * *
1037 TAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTTTTTTCATTGTTTATTGC
1 TAGTGACGTTTTGAATCCTCTTCGATTTGGAAAACCTCAATGCTTTTCTTTCCATTGTTTA-TGC
*
1102 C-TAACTATAATAATTTTGGTGAGATTAGTCCACTGTAAAGTTTTTAGCTCAT
65 CGTAACTATAATAATTTTGGTAAGATTAGTCCACTGTAAAGTTTTTAGCTCAT
1154 AAGGAACACT
Statistics
Matches: 107, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
123 103 0.96
124 4 0.04
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (123 bp):
TAGTGACGTTTTGAATCCTCTTCGATTTGGAAAACCTCAATGCTTTTCTTTCCATTGTTTATGCC
GTAACTATAATAATTTTGGTAAGATTAGTCCACTGTAAAGTTTTTAGCTCATTTGGAA
Found at i:1263 original size:277 final size:276
Alignment explanation
Indices: 762--1313 Score: 863
Period size: 277 Copynumber: 2.0 Consensus size: 276
752 GGGGCCCATA
762 AGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTTTTCCATTCTTTATGGCCT
1 AGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTTTTCCATTCTTTATGGCCT
* * * ** *
827 AACTATAATCATTCTGGTGAGATTAGTCAACTGTGACGTTTTTAGCTCATTTGGAACTCTTGATA
66 AACTATAATAATTCTGGTGAGATTAGTCAACTGTAAAGTTTTTAGCTCATAAGGAACACTTGATA
* * *
892 TTTTGGGCCTATTGGGGCCCATTAGTGACGTTTTGAATCCTCTTCGATTTGGAAAACCTCAATGC
131 CTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCCTCTTCGATTTGGAAAACCCCAATGC
* * *
957 TTTTCTTTCCATTGTTTATGCCGTAACTATGATCCTTTTGGTAAGATTAGTCCACTGTGAAGTTT
196 TTTTCTTTCCATTGTTTATGCCGTAACTATAATCATTTTGGTAAGATTAGTCCACTGGGAAGTTT
1022 TTAGCTCATTTGGAAT
261 TTAGCTCATTTGGAAT
* * *
1038 AGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTTTTTTCATTGTTTATTGCC
1 AGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGC-TTTTTTTCCATTCTTTATGGCC
* * *
1103 TAACTATAATAATTTTGGTGAGATTAGTCCACTGTAAAGTTTTTAGCTCATAAGGAACACTTGTT
65 TAACTATAATAATTCTGGTGAGATTAGTCAACTGTAAAGTTTTTAGCTCATAAGGAACACTTGAT
* ** * *
1168 ACTTTGGGCCTATCGGGGCCCGTTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATG
130 ACTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCCTCTTCGATTTGGAAAACCCCAATG
*
1233 CTTTTCTTTCCATTGTTTATGGCC-TAACTATAATCATTTTGGTGAGATTAGTCCACTGGGAAGT
195 CTTTTCTTTCCATTGTTTAT-GCCGTAACTATAATCATTTTGGTAAGATTAGTCCACTGGGAAGT
1297 TTTTAGCTCATTTGGAA
259 TTTTAGCTCATTTGGAA
1314 CACTTGTTAT
Statistics
Matches: 250, Mismatches: 24, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
276 42 0.17
277 205 0.82
278 3 0.01
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (276 bp):
AGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTTTTCCATTCTTTATGGCCT
AACTATAATAATTCTGGTGAGATTAGTCAACTGTAAAGTTTTTAGCTCATAAGGAACACTTGATA
CTTTGGGCCTATCGGGGCCCATTAGTGACGTTTTGAATCCTCTTCGATTTGGAAAACCCCAATGC
TTTTCTTTCCATTGTTTATGCCGTAACTATAATCATTTTGGTAAGATTAGTCCACTGGGAAGTTT
TTAGCTCATTTGGAAT
Found at i:1328 original size:154 final size:154
Alignment explanation
Indices: 1037--1774 Score: 1156
Period size: 154 Copynumber: 4.8 Consensus size: 154
1027 TCATTTGGAA
* * * * *
1037 TAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTTTTTTCATTGTTTATTGC
1 TAGTTACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
* * **
1102 CTAACTATAATAATTTTGGTGAGATTAGTCCACTGTAAAGTTTTTAGCTCATAAGGAACACTTGT
66 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
*
1167 TACTTTGGGCCTATCGGGGCCCGT
131 TACTTTGGGCCTATCGGGGCCCAT
*
1191 TAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
1 TAGTTACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
*
1256 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAGCTCATTTGGAACACTTGT
66 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
* *
1321 TATTTTGGGCCTATTGGGGCCCAT
131 TACTTTGGGCCTATCGGGGCCCAT
* * * ** *
1345 TAGTGACGTTTTGTATCCTCTTCGATTTGGCATGCCACAATGCTTTTCTTTCCATTGTTTATGGC
1 TAGTTACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
* * * *
1410 CTATCTATAATCCTTTTGGTGAG-GTAGTCCACTGTGAAGTTTTTATCTCATTTGGAACACTTGT
66 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
* * *
1474 TATTTTGGGCATTTCGGGGCCCAT
131 TACTTTGGGCCTATCGGGGCCCAT
* * * *
1498 TA-TTGACGTTTTGAATCGTCTTCGATATGGCAAACCTCAATACTTTTTTTTCCATTGTTTATGG
1 TAGTT-ACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGG
1562 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
65 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
1627 TTACTTTGGGCCTATCGGGGCCCAT
130 TTACTTTGGGCCTATCGGGGCCCAT
*
1652 TAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
1 TAGTTACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
*
1717 CTAACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
66 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
1775 TAGTGACGTT
Statistics
Matches: 530, Mismatches: 51, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
152 1 0.00
153 134 0.25
154 393 0.74
155 2 0.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (154 bp):
TAGTTACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
TACTTTGGGCCTATCGGGGCCCAT
Found at i:1592 original size:307 final size:308
Alignment explanation
Indices: 1037--1774 Score: 1174
Period size: 307 Copynumber: 2.4 Consensus size: 308
1027 TCATTTGGAA
* * * *
1037 TAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTTTTTTCATTGTTTATTGC
1 TAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATGGC
** * **
1102 CTAACTATAATAATTTTGGTGAGATTAGTCCACTGTAAAGTTTTTAGCTCATAAGGAACACTTGT
66 CTAACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
* * * *
1167 TACTTTGGGCCTATCGGGGCCCGTTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCCCAAT
131 TACTTTGGGCATATCGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGATATGGCAAACCCCAAT
*
1232 GCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGGGAAGT
196 ACTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGGGAAGT
* *
1297 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATTGGGGCCCAT
261 TTTTAGCTCATTTGGAACACTTGTTACTTTGGGCCTATCGGGGCCCAT
* * **
1345 TAGTGACGTTTTGTATCCTCTTCGATTTGGCATGCCACAATGCTTTTCTTTCCATTGTTTATGGC
1 TAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATGGC
* * *
1410 CTATCTATAATCCTTTTGGTGAG-GTAGTCCACTGTGAAGTTTTTATCTCATTTGGAACACTTGT
66 CTAACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
* * *
1474 TATTTTGGGCATTTCGGGGCCCATTA-TTGACGTTTTGAATCGTCTTCGATATGGCAAACCTCAA
131 TACTTTGGGCATATCGGGGCCCATTAGTT-ACGTTTTGAATCGTCTTCGATATGGCAAACCCCAA
* *
1538 TACTTTTTTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAG
195 TACTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGGGAAG
1603 TTTTTAGCTCATTTGGAACACTTGTTACTTTGGGCCTATCGGGGCCCAT
260 TTTTTAGCTCATTTGGAACACTTGTTACTTTGGGCCTATCGGGGCCCAT
** *
1652 TAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
1 TAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATGGC
1717 CTAACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
66 CTAACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
1775 TAGTGACGTT
Statistics
Matches: 390, Mismatches: 38, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
306 2 0.01
307 279 0.72
308 109 0.28
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (308 bp):
TAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATGGC
CTAACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
TACTTTGGGCATATCGGGGCCCATTAGTTACGTTTTGAATCGTCTTCGATATGGCAAACCCCAAT
ACTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGGGAAGT
TTTTAGCTCATTTGGAACACTTGTTACTTTGGGCCTATCGGGGCCCAT
Found at i:1878 original size:125 final size:123
Alignment explanation
Indices: 1658--1899 Score: 439
Period size: 125 Copynumber: 2.0 Consensus size: 123
1648 CCATTAGTTC
*
1658 CGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACT
1 CGTTTTGAATCGTCTTCGATTTGGCAAACACCAATGCTTTTCTTTCCATTGTTTATGGCCTAACT
1723 ATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAATAGTGA
66 ATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAATAGTGA
* *
1781 CGTTTTGAATCGTCTTCGATTTGGCAAACATCAATGCTTTTTGTTTTCCATTGTTTATGGCCTAA
1 CGTTTTGAATCGTCTTCGATTTGGCAAACACCAATGC-TTTT-CTTTCCATTGTTTATGGCCTAA
1846 CTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
64 CTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
1900 CACTTGTTAT
Statistics
Matches: 114, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
123 35 0.31
124 4 0.04
125 75 0.66
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.42
Consensus pattern (123 bp):
CGTTTTGAATCGTCTTCGATTTGGCAAACACCAATGCTTTTCTTTCCATTGTTTATGGCCTAACT
ATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAATAGTGA
Found at i:2057 original size:154 final size:154
Alignment explanation
Indices: 1775--2975 Score: 1829
Period size: 154 Copynumber: 7.8 Consensus size: 154
1765 TCATTTGGAA
** *
1775 TAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACATCAATGCTTTTTGTTTTCCATTGTTTATG
1 TAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGC-TTTT-CTTTCCATTGTTTATG
*
1840 GCCTAACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTT
64 GCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTT
*
1905 GTTATTTTGGGCCTATCGGGGCCCAT
129 GTTATTTTGGGCCTTTCGGGGCCCAT
1931 TAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
1 TAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
1996 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
66 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
* *
2061 TATCTTGGGCCTTTCGTGGCCCAT
131 TATTTTGGGCCTTTCGGGGCCCAT
* ** *
2085 TCGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTT-TCTTCCATTGTTTATGG
1 TAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCT-TTCCATTGTTTATGG
*
2149 CCTAACTATAATCATTTGGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
65 CCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTG
* *
2214 TTATCTTGGGCCTTTCGTGGCCCAT
130 TTATTTTGGGCCTTTCGGGGCCCAT
* ** * *
2239 TCGTTCCGTTTTGAATCGCCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCAATTGTTTATGGC
1 TAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
* *
2304 CTAACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACCTGT
66 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
* *
2369 TATTTTGGGCCTTTCGGAGCACAT
131 TATTTTGGGCCTTTCGGGGCCCAT
* ** * * * * *
2393 TCGTTCCGTGTTGAATCGCCTTCGATTTGGCAAACCCTAATGCTTTTCTTTCAATTGTTTGTGGC
1 TAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
* * *
2458 CAAACTATAATCCTTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAGCTCATTTGGAACACTTGT
66 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
2523 TATTTTGGGCCTATT-GGGGCCCAT
131 TATTTTGGGCCT-TTCGGGGCCCAT
* ** *
2547 TAGTGACGTTTTGAATCCTCTTCGATTTGGCAAACCAAAATGCTTTTCATTCCATTGTTTATGGC
1 TAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
* * *
2612 CTAACTATAATCCTTTTGGTGAGA-TAGTCCACTGTGAAGTTTTTATCTCATTTAGAACACTTGT
66 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
* *
2676 TATTTTGGGCATTTCGGTGCCCAT
131 TATTTTGGGCCTTTCGGGGCCCAT
* * **
2700 TAGTGACGTTTTGAATCATCTTCGCTTTGGCAAACTGCAATGCTTTT-TTTCCATTGTTTATGGC
1 TAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
*
2764 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAGCTCATTTGGAACACTTGT
66 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
**
2829 TATTTTGGGCCTACCGGGG-CCAGT
131 TATTTTGGGCCTTTCGGGGCCCA-T
** *
2853 TAGTTCCGTTTTGAATCGTCTTCGATTTGGCATACCCCAATGCTTTTCTTTCCATTGTTTATGGC
1 TAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
2918 CTAACTATAAT-ACTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
66 CTAACTATAATCA-TTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
2976 TAGTGAGGTT
Statistics
Matches: 968, Mismatches: 69, Indels: 18
0.92 0.07 0.02
Matches are distributed among these distances:
152 44 0.05
153 193 0.20
154 683 0.71
155 7 0.01
156 41 0.04
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (154 bp):
TAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
TATTTTGGGCCTTTCGGGGCCCAT
Found at i:3079 original size:123 final size:123
Alignment explanation
Indices: 2860--3098 Score: 451
Period size: 123 Copynumber: 1.9 Consensus size: 123
2850 AGTTAGTTCC
*
2860 GTTTTGAATCGTCTTCGATTTGGCATACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTA
1 GTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTA
2925 TAATACTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAATAGTGAG
66 TAATACTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAATAGTGAG
2983 GTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTA
1 GTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTA
* *
3048 TAATCCTTTTGGTGAGATTAGTCTACTGTGAAGTTTTTAGCTCATTTGGAA
66 TAATACTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
3099 CAGTTGTTGT
Statistics
Matches: 113, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
123 113 1.00
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.42
Consensus pattern (123 bp):
GTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTA
TAATACTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAATAGTGAG
Found at i:3260 original size:154 final size:154
Alignment explanation
Indices: 2976--3697 Score: 1107
Period size: 154 Copynumber: 4.8 Consensus size: 154
2966 TCATTTGGAA
* *
2976 TAGTGAGGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
1 TAGTGACGTTTTGAATCCTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
* *
3041 CTAACTATAATCCTTTTGGTGAGATTAGTCTACTGTGAAGTTTTTAGCTCATTTGGAACAGTTGT
66 CTAACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
* *
3106 TGTTTTGGGACTATTGGGGCCCAT
131 TATTTTGGGCCTATTGGGGCCCAT
**
3130 TAGTGACGTTTTGAATCCTCTTCGATTTGGCAAACAACAATGCTTTTCTTTCCATTGTTTATGGC
1 TAGTGACGTTTTGAATCCTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
* * * *
3195 CTAACTATAATCATTTGGGTGAGATTAGTTCACTGTGATGTTTTTAGCTCATTTGGAACACTTGT
66 CTAACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
3260 TATTTT-GG---A---------A-
131 TATTTTGGGCCTATTGGGGCCCAT
*
3270 TAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
1 TAGTGACGTTTTGAATCCTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
*
3335 CTAACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTACCTCATTTGGAACACTTGT
66 CTAACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
3400 TATTTTGGGCCT-TTCGGGGCCCAT
131 TATTTTGGGCCTATT-GGGGCCCAT
* * *
3424 TAGTGACGTTTTGAATCATCTTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATAGC
1 TAGTGACGTTTTGAATCCTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
3489 CTAACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
66 CTAACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
* ** *
3554 TACTTTGGGCCTACCGGGGCCCGT
131 TATTTTGGGCCTATTGGGGCCCAT
**
3578 TAGTTCCGTTTTGAAT-CTCCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGG
1 TAGTGACGTTTTGAATCCT-CTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGG
3642 CCTAACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTG
65 CCTAACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTG
3698 AAATAGTGAC
Statistics
Matches: 519, Mismatches: 32, Indels: 34
0.89 0.05 0.06
Matches are distributed among these distances:
140 128 0.25
141 3 0.01
150 1 0.00
153 4 0.01
154 383 0.74
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (154 bp):
TAGTGACGTTTTGAATCCTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
CTAACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
TATTTTGGGCCTATTGGGGCCCAT
Found at i:3792 original size:277 final size:277
Alignment explanation
Indices: 3424--3970 Score: 873
Period size: 277 Copynumber: 2.0 Consensus size: 277
3414 CGGGGCCCAT
**
3424 TAGTGACGTTTTGAATCATCTTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATAGC
1 TAGTGACGTTTTGAATCATCTTCGATTTCACAAACCACAATGCTTTTCTTTCCATTGTTTATAGC
* * *
3489 CTAACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
66 CTAACTATAATCCTTTTGATGAGATTAGTCAACTGTGAAGTTTTTAACTCATTTGGAACACTTGT
*
3554 TACTTTGGGCCTACCGGGGCCCGTTAGTTCCGTTTTGAATC-TCCTTCGATTTGGCAAACCCCAA
131 TACTTTGGGCCTACCGGGGCCCATTAGTTCCGTTTTGAATCGT-CTTCGATTTGGCAAACCCCAA
* * * *
3618 TGCTTTTCTTT-CCATTGTTTATGGCCTAACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAA
195 TGCTTTT-TTTACCATTGTTTACGGCCTAACTATAATCATTTTGGTGAGATTAGACCACAGTGAA
3682 GTTTTTAGCTCATTTGAAA
259 GTTTTTAGCTCATTTGAAA
* * *
3701 TAGTGACGTTTTGAATCGTCTTCGATTTCACAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
1 TAGTGACGTTTTGAATCATCTTCGATTTCACAAACCACAATGCTTTTCTTTCCATTGTTTATAGC
*
3766 CTAACTATAATCCTTTTGATGAGATTAGTCAACTGTGATGTTTTTAACTCATTTGGAACACTTGT
66 CTAACTATAATCCTTTTGATGAGATTAGTCAACTGTGAAGTTTTTAACTCATTTGGAACACTTGT
* ** * * *
3831 TATTTTGGGCCTTTCGGGGCCCATTCGTTCTGTTTTGAATCGTCTTCGATTTGGCAAACCCCACT
131 TACTTTGGGCCTACCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCCCAAT
*
3896 GCTTTTTTTACCATTGTTTACGGCCTAACTATAATCATTTTGGTTAGATTAGACCACAGTGAAGT
196 GCTTTTTTTACCATTGTTTACGGCCTAACTATAATCATTTTGGTGAGATTAGACCACAGTGAAGT
3961 TTTTAGCTCA
261 TTTTAGCTCA
3971 CTTGGAACAC
Statistics
Matches: 247, Mismatches: 21, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
276 3 0.01
277 243 0.98
278 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (277 bp):
TAGTGACGTTTTGAATCATCTTCGATTTCACAAACCACAATGCTTTTCTTTCCATTGTTTATAGC
CTAACTATAATCCTTTTGATGAGATTAGTCAACTGTGAAGTTTTTAACTCATTTGGAACACTTGT
TACTTTGGGCCTACCGGGGCCCATTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCCCAAT
GCTTTTTTTACCATTGTTTACGGCCTAACTATAATCATTTTGGTGAGATTAGACCACAGTGAAGT
TTTTAGCTCATTTGAAA
Found at i:3803 original size:123 final size:123
Alignment explanation
Indices: 3584--3820 Score: 404
Period size: 123 Copynumber: 1.9 Consensus size: 123
3574 CCGTTAGTTC
**
3584 CGTTTTGAATCTCCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACT
1 CGTTTTGAATCTCCTTCGATTTCACAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACT
* * *
3649 ATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGAAATAGTGA
66 ATAATCCTTTTGATGAGATTAGTCAACTGTGAAGTTTTTAACTCATTTGAAATAGTGA
3707 CGTTTTGAATCGT-CTTCGATTTCACAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAAC
1 CGTTTTGAATC-TCCTTCGATTTCACAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAAC
*
3771 TATAATCCTTTTGATGAGATTAGTCAACTGTGATGTTTTTAACTCATTTG
65 TATAATCCTTTTGATGAGATTAGTCAACTGTGAAGTTTTTAACTCATTTG
3821 GAACACTTGT
Statistics
Matches: 107, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
123 106 0.99
124 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.42
Consensus pattern (123 bp):
CGTTTTGAATCTCCTTCGATTTCACAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACT
ATAATCCTTTTGATGAGATTAGTCAACTGTGAAGTTTTTAACTCATTTGAAATAGTGA
Found at i:3988 original size:154 final size:154
Alignment explanation
Indices: 3701--4280 Score: 853
Period size: 154 Copynumber: 3.8 Consensus size: 154
3691 TCATTTGAAA
* **
3701 TAGTGACGTTTTGAATCGTCTTCGATTTCACAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
1 TAGTAACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
* * * * *
3766 CTAACTATAATCCTTTTGATGAGATTAGTCAACTGTGATGTTTTTAACTCATTTGGAACACTTGT
66 CTAACTATAATCCTTTTGGTGAGATTAGTCCACAGTGAAGTTTTTAGCTCATTTGGAACACTTGT
3831 TATTTTGGGCCTTTCGGGGCCCAT
131 TATTTTGGGCCTTTCGGGGCCCAT
* * * *
3855 TCGT-TCTGTTTTGAATCGTCTTCGATTTGGCAAACCCCACTGCTTTT-TTTACCATTGTTTACG
1 TAGTAAC-GTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTT-CCATTGTTTATG
* * * *
3918 GCCTAACTATAATCATTTTGGTTAGATTAGACCACAGTGAAGTTTTTAGCTCACTTGGAACACTT
64 GCCTAACTATAATCCTTTTGGTGAGATTAGTCCACAGTGAAGTTTTTAGCTCATTTGGAACACTT
*
3983 GTTATTTTGGGCCTATTC-GGGCCCGT
129 GTTATTTTGGGCCT-TTCGGGGCCCAT
* * * * *
4009 TAGTAACGTTTTGAATCATTTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTGAAGGC
1 TAGTAACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
*
4074 CTAACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
66 CTAACTATAATCCTTTTGGTGAGATTAGTCCACAGTGAAGTTTTTAGCTCATTTGGAACACTTGT
4139 TATTTTGGGCCTTTCGGGGCCCAT
131 TATTTTGGGCCTTTCGGGGCCCAT
* * * *
4163 TAGTGACGATTTGAATCCTCTTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTATGGC
1 TAGTAACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
4228 CTAACTATAATCCTTTTGGTGAGATTAGTCCACTA-TGAAGTTTTTAGCTCATT
66 CTAACTATAATCCTTTTGGTGAGATTAGTCCAC-AGTGAAGTTTTTAGCTCATT
4281 ATTGGCCTCT
Statistics
Matches: 381, Mismatches: 38, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
153 7 0.02
154 367 0.96
155 7 0.02
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (154 bp):
TAGTAACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
CTAACTATAATCCTTTTGGTGAGATTAGTCCACAGTGAAGTTTTTAGCTCATTTGGAACACTTGT
TATTTTGGGCCTTTCGGGGCCCAT
Found at i:4077 original size:431 final size:431
Alignment explanation
Indices: 607--4128 Score: 2528
Period size: 431 Copynumber: 8.0 Consensus size: 431
597 TGGGGACCAT
* ** **
607 TAGTGACGTTTTGAATCCTCTTCGATTTGGCAAACCATAATGCTTTTCTTTCCATTGTTTATGGC
1 TAGTGACGTTTTGAATCGTCTTCGATTTCACAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
* * * *
672 CTAACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACATGT
66 CTAACTATAATCCTTTTGATGAGATTAGTCAACTGTGAAGTTTTTAACTCATTTGGAACACTTGT
* * * *
737 TATTTTGGGCATTTCGGGGCCCATAAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAT
131 TATTTTGGGCCTTTCGGGGCCCATTAGTGACGTTTTGAATCATCTTCGATTTGGCAAACCACAAT
* ** * * * * *
802 GCTTTT-TTTCCATTCTTTATGGCCTAACTATAATCATTCTGGTGAGATTAGTCAACTGTGACGT
196 GCTTTTCTTTCCATTGTTTACAGCCTAACTATAATCATTTTGGTGAGATTAGACCACAGTGAAGT
* * * * ** * *
866 TTTTAGCTCATTTGGAACTCTTGATATTTTGGGCCTATTGGGGCCCATTAGTGACGTTTTGAATC
261 TTTTAGCTCACTTGGAACACTTGTTACTTTGGGCCTACCGGGGCCCGTTAGTAACGTTTTGAATC
* * * * *
931 -CTCTTCGATTTGGAAAACCTCAATGCTTTTCTTTCCATTGTT-TATGCCGTAACTATGATCCTT
326 TC-CTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTGAAGGCC-TAACTATAATCCTT
* *
994 TTGGTAAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAA
389 TTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGAAA
** * * * *
1037 TAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCTCAATGCTTTTTTTTTCATTGTTTATTGC
1 TAGTGACGTTTTGAATCGTCTTCGATTTCACAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
** * * * * **
1102 CTAACTATAATAATTTTGGTGAGATTAGTCCACTGTAAAGTTTTTAGCTCATAAGGAACACTTGT
66 CTAACTATAATCCTTTTGATGAGATTAGTCAACTGTGAAGTTTTTAACTCATTTGGAACACTTGT
* * * ** * *
1167 TACTTTGGGCCTATCGGGGCCCGTTAGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCCCAAT
131 TATTTTGGGCCTTTCGGGGCCCATTAGTGACGTTTTGAATCATCTTCGATTTGGCAAACCACAAT
** * * *
1232 GCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGGGAAGT
196 GCTTTTCTTTCCATTGTTTACAGCCTAACTATAATCATTTTGGTGAGATTAGACCACAGTGAAGT
* * ** * * *
1297 TTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATTGGGGCCCATTAGTGACGTTTTGTATC
261 TTTTAGCTCACTTGGAACACTTGTTACTTTGGGCCTACCGGGGCCCGTTAGTAACGTTTTGAATC
** * * * *
1362 -CTCTTCGATTTGGCATGCCACAATGCTTTTCTTTCCATTGTTTATGGCCTATCTATAATCCTTT
326 TC-CTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTGAAGGCCTAACTATAATCCTTT
* *
1426 TGGTGAG-GTAGTCCACTGTGAAGTTTTTATCTCATTTGGAACACTTGTTA
390 TGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTT-G-A-A------A
* ** * *
1476 TTTTGGGCATTTCGGGGCCCATTATTGACGTTTTGAATCGTCTTCGATATGGCAAACCTCAATAC
1 ---T----A-------G--------TGACGTTTTGAATCGTCTTCGATTTCACAAACCCCAATGC
* * * *
1541 TTTTTTTTCCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTT
44 TTTTCTTTCCATTGTTTATGGCCTAACTATAATCCTTTTGATGAGATTAGTCAACTGTGAAGTTT
* * * ** *
1606 TTAGCTCATTTGGAACACTTGTTACTTTGGGCCTATCGGGGCCCATTAGTTCCGTTTTGAATCGT
109 TTAACTCATTTGGAACACTTGTTATTTTGGGCCTTTCGGGGCCCATTAGTGACGTTTTGAATCAT
* ** *
1671 CTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCCTTTTGG
174 CTTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTACAGCCTAACTATAATCATTTTGG
* * * * * * * *
1736 TGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGG-A-A-TAGTGACGTTTTGAATCGTCT-T
239 TGAGATTAGACCACAGTGAAGTTTTTAGCTCACTTGGAACACTTGTTAC--TTTG---GGCCTAC
* * * * * * * * * * * *** *
1797 CGATTTGGCAAACATCAAT-GCTTTTTG-TTTTCCATT-GTTTATGGCCTAACTATAATCCTTTT
299 CG---GGGC--CCGTTAGTAACGTTTTGAATCTCC-TTCGATT-TGG-CAAACCCCAATGCTTTT
** * * * * * * * ** *
1859 -GGT-GA--GATT--AGTCC--ACTGTGAAGT--TTTTAGCTCA-TTTGGAACACT-TGTTA-TT
356 CTTTCCATTG-TTGAAGGCCTAACTAT-AA-TCCTTTT-GGTGAGATTAGTCCACTGTG-AAGTT
** ** * *
1911 TTGGGC-CTATCGGGGCCCAT
416 TTTAGCTC-AT--TTG--AAA
**
1931 TAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
1 TAGTGACGTTTTGAATCGTCTTCGATTTCACAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
* * * *
1996 CTAACTATAATCATTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACACTTGT
66 CTAACTATAATCCTTTTGATGAGATTAGTCAACTGTGAAGTTTTTAACTCATTTGGAACACTTGT
* * * ** * *
2061 TATCTTGGGCCTTTCGTGGCCCATTCGTTCCGTTTTGAATCGTCTTCGATTTGGCAAACCTCAAT
131 TATTTTGGGCCTTTCGGGGCCCATTAGTGACGTTTTGAATCATCTTCGATTTGGCAAACCACAAT
** * * *
2126 GCTTTT-TCTTCCATTGTTTATGGCCTAACTATAATCATTTGGGTGAGATTAGTCCACTGTGAAG
196 GCTTTTCT-TTCCATTGTTTACAGCCTAACTATAATCATTTTGGTGAGATTAGACCACAGTGAAG
* ** * * * **
2190 TTTTTAGCTCATTTGGAACACTTGTTA-TCTTGGGCCTTTCGTGGCCCATTCGTTCCGTTTTGAA
260 TTTTTAGCTCACTTGGAACACTTGTTACT-TTGGGCCTACCGGGGCCCGTTAGTAACGTTTTGAA
* * * *
2254 TCGCCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCAATTGTTTATGGCCTAACTATAATCCTT
324 TCTCCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTGAAGGCCTAACTATAATCCTT
2319 TTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGGAACA
389 TTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTT-GAA-A
* **
2364 CCTGTTATTTTGGGCCTTTCGGAGCACATTCGTTCCGTGTTGAATCGCCTTCGATTTGGCAAACC
1 -----TA------G----T----G---A--CG-T---T-TTGAATCGTCTTCGATTTCACAAACC
* * * * * * *
2429 CTAATGCTTTTCTTTCAATTGTTTGTGGCCAAACTATAATCCTTTTGGTGAGATTAGTCCACTGG
37 CCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCCTTTTGATGAGATTAGTCAACTGT
*
2494 GAAGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGGCCTATT-GGGGCCCATTAGTGACGTTT
102 GAAGTTTTTAACTCATTTGGAACACTTGTTATTTTGGGCCT-TTCGGGGCCCATTAGTGACGTTT
* * * **
2558 TGAATCCTCTTCGATTTGGCAAACCAAAATGCTTTTCATTCCATTGTTTATGGCCTAACTATAAT
166 TGAATCATCTTCGATTTGGCAAACCACAATGCTTTTCTTTCCATTGTTTACAGCCTAACTATAAT
* * * * * * * *
2623 CCTTTTGGTGAGA-TAGTCCACTGTGAAGTTTTTATCTCATTTAGAACACTTGTTATTTTGGGCA
231 CATTTTGGTGAGATTAGACCACAGTGAAGTTTTTAGCTCACTTGGAACACTTGTTACTTTGGGCC
** * * * * **
2687 TTTCGGTGCCCATTAGTGACGTTTTGAATCAT-CTTCGCTTTGGCAAACTGCAATGCTTTT-TTT
296 TACCGGGGCCCGTTAGTAACGTTTTGAATC-TCCTTCGATTTGGCAAACCCCAATGCTTTTCTTT
* * * *
2750 CCATTGTTTATGGCCTAACTATAATCATTTTGGTGAGATTAGTCCACTGGGAAGTTTTTAGCTCA
360 CCATTGTTGAAGGCCTAACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCA
2815 TTTGGAACA
425 TTT-GAA-A
** *
2824 CTTGTTATTTTGGGCCTACCGGGGCCAGTTAGTTCCGTTTTGAATCGTCTTCGATTTGGCATACC
1 -----TA------G--T----------G--A----CGTTTTGAATCGTCTTCGATTTCACAAACC
* * *
2889 CCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATACTTTTGGTGAGATTAGTCCACTGT
37 CCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCCTTTTGATGAGATTAGTCAACTGT
* * * *** ** * * ** *
2954 GAAGTTTTTAGCTCATTTGGAATA-GTGAGGTTTTGAATCGTCTTCGATTTGGCAAACC-CCAAT
102 GAAGTTTTTAACTCATTTGGAACACTTGTTATTTTG-GGCCT-TTCG---GGGC---CCATTAGT
*** * * * * * ** * * *
3017 G-C-TTTTCTTTC--CATT-GTTTATGGCCTAACTATAATCCTTTT-GGT-GA--GATT--AGTC
159 GACGTTTTGAATCATC-TTCGATT-TGG-CAAACCACAATGCTTTTCTTTCCATTGTTTACAGCC
* * * * * * * *
3071 T-ACTGTGAAGT--TTTTAGCTCA-TTTGGA--AC-----AGTTGTT-G-T--TTTGG--GAC--
221 TAACTAT-AA-TCATTTT-GGTGAGATTAGACCACAGTGAAGTTTTTAGCTCACTTGGAACACTT
* * **
3117 --TA--TTGGG---------GCCCATTAGTGACGTTTTGAATC-CTCTTCGATTTGGCAAACAAC
283 GTTACTTTGGGCCTACCGGGGCCCGTTAGTAACGTTTTGAATCTC-CTTCGATTTGGCAAACCCC
* * * * *
3168 AATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCATTTGGGTGAGATTAGTTCACTGTGA
347 AATGCTTTTCTTTCCATTGTTGAAGGCCTAACTATAATCCTTTTGGTGAGATTAGTCCACTGTGA
*
3233 TGTTTTTAGCTCATTTGGAACACTTGTTATTTTGGAA
412 AGTTTTTAGCTCA--T-------TTG--A------AA
**
3270 TAGTGACGTTTTGAATCGTCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
1 TAGTGACGTTTTGAATCGTCTTCGATTTCACAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
* * *
3335 CTAACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGTTTTTACCTCATTTGGAACACTTGT
66 CTAACTATAATCCTTTTGATGAGATTAGTCAACTGTGAAGTTTTTAACTCATTTGGAACACTTGT
3400 TATTTTGGGCCTTTCGGGGCCCATTAGTGACGTTTTGAATCATCTTCGATTTGGCAAACCACAAT
131 TATTTTGGGCCTTTCGGGGCCCATTAGTGACGTTTTGAATCATCTTCGATTTGGCAAACCACAAT
* * * *
3465 GCTTTTCTTTCCATTGTTTATAGCCTAACTATAATCCTTTTGGTGAGATTAGTCCACTGTGAAGT
196 GCTTTTCTTTCCATTGTTTACAGCCTAACTATAATCATTTTGGTGAGATTAGACCACAGTGAAGT
* **
3530 TTTTAGCTCATTTGGAACACTTGTTACTTTGGGCCTACCGGGGCCCGTTAGTTCCGTTTTGAATC
261 TTTTAGCTCACTTGGAACACTTGTTACTTTGGGCCTACCGGGGCCCGTTAGTAACGTTTTGAATC
* *
3595 TCCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTTATGGCCTAACTATAATCCTTTT
326 TCCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTGAAGGCCTAACTATAATCCTTTT
3660 GGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGAAA
391 GGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGAAA
3701 TAGTGACGTTTTGAATCGTCTTCGATTTCACAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
1 TAGTGACGTTTTGAATCGTCTTCGATTTCACAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
*
3766 CTAACTATAATCCTTTTGATGAGATTAGTCAACTGTGATGTTTTTAACTCATTTGGAACACTTGT
66 CTAACTATAATCCTTTTGATGAGATTAGTCAACTGTGAAGTTTTTAACTCATTTGGAACACTTGT
* * * * *
3831 TATTTTGGGCCTTTCGGGGCCCATTCGT-TCTGTTTTGAATCGTCTTCGATTTGGCAAACCCCAC
131 TATTTTGGGCCTTTCGGGGCCCATTAGTGAC-GTTTTGAATCATCTTCGATTTGGCAAACCACAA
* *
3895 TGCTTTT-TTTACCATTGTTTACGGCCTAACTATAATCATTTTGGTTAGATTAGACCACAGTGAA
195 TGCTTTTCTTT-CCATTGTTTACAGCCTAACTATAATCATTTTGGTGAGATTAGACCACAGTGAA
* *
3959 GTTTTTAGCTCACTTGGAACACTTGTTATTTTGGGCCTATTC-GGGCCCGTTAGTAACGTTTTGA
259 GTTTTTAGCTCACTTGGAACACTTGTTACTTTGGGCCTA-CCGGGGCCCGTTAGTAACGTTTTGA
* *
4023 ATCAT-TTTCGATTTGGCAAACCTCAATGCTTTTCTTTCCATTGTTGAAGGCCTAACTATAATCC
323 ATC-TCCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTGAAGGCCTAACTATAATCC
4087 TTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTG
387 TTTTGGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTG
4129 GAACACTTGT
Statistics
Matches: 2574, Mismatches: 310, Indels: 415
0.78 0.09 0.13
Matches are distributed among these distances:
410 2 0.00
411 3 0.00
412 1 0.00
413 22 0.01
414 6 0.00
415 5 0.00
416 4 0.00
417 120 0.05
418 8 0.00
419 9 0.00
420 11 0.00
421 1 0.00
422 2 0.00
423 1 0.00
427 22 0.01
428 13 0.01
429 12 0.00
430 263 0.10
431 640 0.25
432 14 0.01
433 269 0.10
434 21 0.01
435 12 0.00
436 5 0.00
437 3 0.00
438 2 0.00
439 15 0.01
440 2 0.00
441 6 0.00
442 1 0.00
444 1 0.00
445 2 0.00
446 3 0.00
447 5 0.00
448 113 0.04
449 2 0.00
451 6 0.00
452 2 0.00
453 1 0.00
455 1 0.00
456 2 0.00
457 10 0.00
458 16 0.01
459 10 0.00
460 221 0.09
461 374 0.15
462 223 0.09
463 13 0.01
464 27 0.01
465 13 0.01
466 16 0.01
467 18 0.01
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (431 bp):
TAGTGACGTTTTGAATCGTCTTCGATTTCACAAACCCCAATGCTTTTCTTTCCATTGTTTATGGC
CTAACTATAATCCTTTTGATGAGATTAGTCAACTGTGAAGTTTTTAACTCATTTGGAACACTTGT
TATTTTGGGCCTTTCGGGGCCCATTAGTGACGTTTTGAATCATCTTCGATTTGGCAAACCACAAT
GCTTTTCTTTCCATTGTTTACAGCCTAACTATAATCATTTTGGTGAGATTAGACCACAGTGAAGT
TTTTAGCTCACTTGGAACACTTGTTACTTTGGGCCTACCGGGGCCCGTTAGTAACGTTTTGAATC
TCCTTCGATTTGGCAAACCCCAATGCTTTTCTTTCCATTGTTGAAGGCCTAACTATAATCCTTTT
GGTGAGATTAGTCCACTGTGAAGTTTTTAGCTCATTTGAAA
Found at i:5683 original size:25 final size:24
Alignment explanation
Indices: 5646--5692 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
5636 TTGAAAATTT
5646 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGAT-GAT-AGATGGA
5672 TGAAAAAC-TTGATGATAGATG
1 TGAAAAACTTTGATGATAGATG
5693 AATAGAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (24 bp):
TGAAAAACTTTGATGATAGATGGA
Found at i:11564 original size:16 final size:17
Alignment explanation
Indices: 11537--11574 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
11527 TTTTTTTGTA
11537 TTTTTGCTATTTCCATT
1 TTTTTGCTATTTCCATT
*
11554 TTTTTGC-ATTTGCATT
1 TTTTTGCTATTTCCATT
11570 TTTTT
1 TTTTT
11575 TGTATTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.11, C:0.13, G:0.08, T:0.68
Consensus pattern (17 bp):
TTTTTGCTATTTCCATT
Found at i:11581 original size:17 final size:16
Alignment explanation
Indices: 11537--11581 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
11527 TTTTTTTGTA
11537 TTTTTGCTATTTCCATT
1 TTTTTG-TATTTCCATT
* *
11554 TTTTTGCATTTGCATTT
1 TTTTTGTATTTCCA-TT
11571 TTTTTGTATTT
1 TTTTTGTATTT
11582 TCTAAATGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.11, C:0.11, G:0.09, T:0.69
Consensus pattern (16 bp):
TTTTTGTATTTCCATT
Done.